(Keep in mind that the point in learning counterpoint is not to teach you how to write in a 17th century style, which is a common misconception. If you read the works of Heinrich Schenker, you'll find that a lot of the greatest classical works when simplified using Schenker's techniques read as perfect species counterpoint. Studying strict counterpoint and doing the exercises naturally strengthens your ability to write with good voice leading in your free compositions wherever you feel it's necessary.)
If you're reading this, I assume you're interested in becoming a composer. My advice to you is this; DON'T. Unless you can't live without music, unless you feel that there's absolutely nothing else in the world you'd rather do, unless you need several hours of your favorite composer/artist every day to simply live, don't bother.
Composition is a very unrewarding, very difficult, very lonely, and often very unfulfilling line of work. If you wish to become a composer, you are in for years and years of unavoidably tortuous (not an exaggeration), monotonous, soul-crushing mental training, and after all of this, there is absolutely no guarantee of success. 99.9% of people in this field die unfulfilled in poverty and obscurity.
Don't believe me? JS Bach's works were almost completely disregarded and forgotten about until ~80 years after his death. Here is one of Mozart's many heartbreaking letters in his final years, begging for money to keep himself afloat:
Great God! I would not wish my worst enemy to be in my present position. And if you, most beloved friend and brother, forsake me, we are altogether lost, both my unfortunate and blameless self and my poor sick wife and child. Only the other day when I was with you I was longing to open my heart to you, but I had not the courage to do so and indeed I should still not have the courage for, as it is, I only dare to write and tremble as I do so and I should not even dare to write, were I not certain that you know me, that you are aware of my circumstances, and that you are wholly convinced of my innocence so far as my unfortunate and most distressing situation is concerned.
Good God! I am coming to you not with thanks but with fresh entreaties! Instead of paying my debts I am asking for more money! If you really know me, you must sympathise with my anguish in having to do so. I need not tell you once more that owing to my unfortunate illness I have been prevented from earning anything. But I must mention that in spite of my wretched condition I decided to give subscription concerts at home in order to be able to meet at least my present great and frequent expenses, for I was absolutely convinced of your friendly assistance. But even this has failed. Unfortunately Fate is so much against me, though only in Vienna, that even when I want to, I cannot make any money. A fortnight ago I sent round a list for subscribers and so far the only name on it is that of Baron van Swieten! Now that (the 13th) my dear little wife seems to be improving every day, I should be able to set to work again, if this blow, this heavy blow, had not come. At any rate, people are consoling me by telling me that she is better although the night before last she was suffering so much and I on her account that I was stunned and despairing. But last night (the I4th), she slept so well and has felt so much easier all the morning that I am very hopeful; and at last I am beginning to feel inclined for work. I am now faced, however, with misfortunes of another kind, though, it is true, only for the moment.
Dearest, most beloved friend and brother you know my present circumstances, but you also know my prospects. So let things remain as we arranged; that is, thus or thus, you understand what I mean. Meanwhile I am composing six easy clavier sonatas for Princess Friederike J and six quartets for the King of Prussia, 2 all of which Kozeluch is engraving at my expense. At the same time the two dedications will bring me in something. In a month or two my fate must be decided in every detail. Therefore, most beloved friend, you will not be risking anything so far as I am concerned. So it all depends, my only friend, upon whether you will or can lend me another 500 gulden.
Until my affairs are settled, I undertake to pay back ten gulden a month; and then, as this is bound to happen in a few months, I shall pay back the whole sum with whatever interest you may demand, and at the same time acknowledge myself to be your debtor for life. That, alas, I shall have to remain, for I shall never be able to thank you sufficiently for your friendship and affection. Thank God, that is over. Now you know all. Do not be offended by my confiding in you and remember that unless you help me, the honour, the peace of mind, and perhaps the very life of your friend and brother Mason will be ruined.
Ever your most grateful servant, true
friend and brother
W. A. MOZART
At home, July 14th, 1789.
Chopin died of tuberculosis at the age of 39 forgotten, and in poverty. Schubert was never noticed in his lifetime (he was only first discovered by Schumann nearly 20 years after his death), and died of syphilis in poverty at the age of 31. Schumann despaired so much about the quality of his own music that he attempted to commit suicide by drowning himself in the Rhine at the age of 44, and he died two years later in a mental asylum.
Are you still willing to go through with this?
Go to the keyboard now and improvise a fugue in the style of Bach on whatever theme you like. Can't do that? Go to the keyboard and play a whole tone scale in the bass starting on E-flat, and harmonize it in the treble with minor seventh chords (according to the rules of voice leading, of course), and we'll see what it sounds like. No? Go to the keyboard and play the first prelude of Bach's Well Tempered Clavier transposed to A-flat major. Can you not do that? If I play you an aria from a Mozart opera, will you be able to transcribe it after one hearing? No? Can you realize a simple figured bass? Can you even play a C major scale with the proper fingering? Do you even have a keyboard?
You might think that all of this sounds very unnecessary and that I'm expecting you to perform miracles, but unfortunately these sorts of things are the minimum that's expected of you. To be effective as a musician and a composer, music should be as fluent to you as language is to everyone else. Would you not expect an author to do the equivalent of these things with language? Most people think of these things as something only a genius or a very talented person can do (and of course we don't mind that ;>), but in reality, it's basic competence.
As a musician, you are expected to be the culmination in a line of ~100,000 years worth of musicians. Unless you can eventually offer something to the world as valuable as a work by JS Bach, Mozart, Beethoven et. al. what's the point in even bothering? Your life would probably be much better spent as a charity worker or a labourer if you can't do that. We have millions of hours of music already (most of which is garbage) and frankly, the world likely won't miss yours.
Do you still want to become a composer? If you do, God help you and read on, and don't make too many plans for the next decade or so...
I'd recommend at minimum dedicating at least 15 to 30 minutes to this every day (at most an hour or two). Get yourself into a schedule that you can keep up for the next few years, and be sure to continue composing outside of your education.
Start out with these to get your feet wet, and to become familiar and comfortable with how music is discussed:
Now the real fun begins. You need to start by training your ears (you should be able to identify types of chords by sight/ear, identify pitches by sight/ear, keys etc. etc.) and becoming competent at playing the keyboard. With regards to playing the keyboard, there's really no way around this. You can try training yourself on something like the guitar (as Berlioz did) if you really want to, but you're sort of shooting yourself in the foot. Buy a cheap MIDI controller and plug it into FL studio and you're off. (The MIDI controller I use is an Oxygen 88, if you're interested). If you're questioning whether or not you need to be able to play at all, imagine an author who's unable to speak.
The goal here is not to train you to write in the style of Palestrina (though that is a side effect), it is rather to train your subconscious mind to treat each line as an independent living voice, and in order to get each voice to interact in such a way that the music is always pure and interesting to the ears. Music written with this foundation will flow through the listener's mind with ease and fluency. It is a strong, invisible and transparent foundation upon which you can express yourself with absolute fluency no matter what style you're writing in, and it's been this way (in the Western world) for the past 500 years.
In addition to studying counterpoint, you must also study harmony. The tried and true method is by learning how to realize figured basses (at sight on the keyboard, and on paper in both open and closed score, which you can do in the Counterpointer software), which JS Bach himself explains here: http://normanschmidt.net/scores/bachjs-general_bass_rules.pdf
In addition to all of this, the rest of your life should be dedicated to studying the music of other composers (it really doesn't matter who), and figuring out what makes their music tick, and how you can use their tricks in your own music. I can't really be too specific on how to go about this, but I have some recommendations on where to start so that you can begin to learn how to analyse music yourself:
Use whatever academic resources you can get your hands on, absorb any lectures you find. Read every biography on your favorite composers and figure out their methods of working. Join classical music forums and mailing lists and discuss the issues facing music today with your peers.
Nadia Boulanger was a music theory teacher in the twentieth century, who is known for teaching a huge number of recognizable names in music, including; Aaron Copland, Philip Glass, Daniel Barenboim. She was also close friends with composers such as Leonard Bernstein and Igor Stravinsky, who would often present new works to her for her feedback.