I think I figured out something important while trying to sleep last night.. I don't want to put notes in chords until after voices are done, and chords are only an afterthought for other stuff further down the track.

Notes are grouped on stems etc for a reason, and if two notes overlap on the x axis without being on the same stem, they mustn't be in the same voice. Notes not on stems (semibreve and longer) aren't going to be shorter than a beat, and beats are more important than bars. Since semibreves etc are at least a beat long and (I assume) always on the start of a beat, it won't matter if they are treated as separate voices. Rests might be a bit difficult...