I tend to write in Sibelius, then bounce the MIDI file into protools. From then on I'll just replace each part as and when the opportunity arises. Most of my drum tracks come from easy drummer, whether it's importing loops or a MIDI drum kit (I know, it's cheating, but in my defence, how many drummers do you know who are happy to switch between irregular meters all day?). The guitars are generally done by my brother in his lounge (nice, big room) using Mid/Side mic'ing (generally), then the keys, bass and vocals are done back at mine - usually at my kitchen table - from then on I leave them for a couple of weeks.
When I go back to them if I still like the track/arrangement then I'll push it forwards, if not, then it's one for the "we thought this was all sh*te when he was alive, but now he's dead and we still need to recoup" album that'll be released 'post mortem'.
What a happy thought.