How are your audiation skills?
Write what you're hearing. Yes, you aren't going to get it all. At first you might just get a lead line, and have to discover the harmony after the fact. All good. If you have rhythms but are unsure of harmony, note the rhythms with cluster heads denoting register, then work out the harmony later. Harmony is your chief delineator of larger rhythm, so be aware of the nuances between subtle harmonic change (Cmaj to E min) and extreme (Cmaj to Ab min).

I mainly use paper and pencil to write down my initial ideas. For myself it looks like writing the 4 part harmonies, short polyphonic phrases here and there. Then once I get the gist of the structure, I go over to the software and make final edits there. Paper and pen forced you to write truly what’s on your mind and the “real” ideas in head. Software and playback capabilities can tend to fantasize what you want to compose. Pen and paper is like farm to table ;) and I’m in total agreement with the others, studying Bach and musical scores not to steal there music but to learn how they were effective.

And THANK YOU ALL. There.

I agree about pencil and paper — you have to choose each note purposefully. With software it's too easy to copy-n-paste, or play in stuff with MIDI, so you don't have to think through what you're creating. You can just mess around and see what happens. Good compositions have to be tightly controlled — a purposeful use of a harmonic palette, repetition and development of melodic ideas, formal structure, etc. I use software only for engraving, and wrestle with the act of composition at a desk or a piano.

The other thing I think is absolutely necessary is the regularity of composing often. I've gone through phases where I was cranking out new pieces every week, for periods of 3-4 years at a time, and I usually feel like it takes a few months to shake off all the rust and finally get into the groove (the mojo, if you will) of composing — but then things start to happen. I've always admired the Brazilian composer Hermeto Pascoal, who wrote a tune a day, and would then publish a year's worth of compositions in a big book. Concert band composer W. Francis McBeth said once at a clinic that he squirrels himself away every day from 7-11am and composes; a student asked, "What if musical ideas come to you at other times of day?" and he answered, "that never happens, because my mind is so used to a certain routine for musical creativity." Admirable discipline, that.

You may fear that if you're writing all the time, you'll end up repeating yourself, and while there's some risk of that, I have found that writing regularly at close intervals does the opposite: as I see the musical devices that I tend to gravitate toward, I also begin to tweak and develop them, so that six months down the road my palette has subtly but noticeably expanded.

See what your favorite choral pieces do. Repeat that.