I suppose my answer would be 'when it needs to be changed'. I used prefolds (a version of flat nappies but requires hardly any folding) and at a nappy change I'd pull the cover off, but if bub was dry, I left him!
I used to change mid feed for awhile, to wake him up as he'd fall asleep while feeding! He'd often empty his bowels during a feed or not long after (what goes in, must come out!) so I usually changed him afterwards, unless he'd just pooed beforehand. He settled pretty easily though, so I didn't really have to worry about using the feed to put him to sleep.

I'd say just do whatever seems to work best for you!