I usually wait to cut stuff out until it's in, then I don't find I've cut out any more than I absolutely needed to. The best trick I've found is actually for the screws where they have to go through, like the sill plates. Mark the spot with a soldering iron. Makes them plainly visible so you always know where your hole is, and it corderizes the hole so you can put the screw through it without getting it all bound up in the fibers. Makes taking that stuff back out a sinch too.