Interesting thread.
I like to hear how people get their arrangment down. It's by far the most difficult thing for me too - it's makes or breaks a track.
Anyway....
I tend to start my tracks on the hardware sequencer in my JX305. Once I have a small loop going (usually with 2 sections of melody lines), I jam with it - using the mixer to fade in parts, send FX, EQ on the fly and play with the structure a little. Also while at this stage, I'll play other bits live. From here I'll turn on the computer and record some parts to audio and move other midi lines into cubase. Then I'll always build up the drums - layering by recording straight to audio for each new sound, untill I'll happy.
Because I have already played with the structure a little I know where I want things to happen, but I still get into a copy and paste mentality - this is my downfall.
I think jamming and having fun with tunes helps get your arrangement down, but when switching to a copy and paste system, things start to get more difficult.