Another good notation software (with midi playback) is Personal Composer. I've used it for most of my charts for a long time. There are quite a few clefs, 3 treble clefs, 3 F clefs, 4-5 C clefs.
Band in a Box is also a good tool, it's made to create play-alongs, but you can easily transpose your songs. Note by note entry is awkward, but entering chords is super-easy.
Transposing is kind of a brain-teaser, but you can get used to it. What I do is memorize some reference points (for example, if you have music written for Eb instruments, all the A's are really C's). Then it's not too hard to figure out the odd notes in between.
Here's a quick guide:
Bb instruments to Concert - down 2 or up 10
Eb instruments to Concert - up 3 or down 9
F instruments to Concert - down 7 or up 5
Make yourself a chart showing the 12 notes for each transposition, then you can use it when you're stuck. And you can go in the other direction if you want to, say, make a chart for a clarinet player. Something like this:
C = Bb Eb F
B = A E E
Bb = C F Eb
etc.
Then learn which instruments are Bb, Eb, F , or other. Clarinets and Saxes are either Bb or Eb, French Horn is F, English Horn is F, etc.
What you really need, that you can't get from software packages, is knowledge of the ranges and transposition of all the instruments on your scores. I have a great book by Tom Bruner called
"Basic Concepts of Arranging and Orchestrating Music" (published by Mel Bay). It gives this info for every instrument imaginable. It also gives simple guidelines for arranging, but it leaves most of that to your taste.
There's no substitute for sitting down and charting it all out.