Playhouse roof - lining up the rafters

http://ana-white.com/2010/05/playhouse-roof

We are putting this together up on the deck tonight, so don't know if anyone will see this in time. But my question is, the instructions say to line up the rafter with the joists in the back wall, and screw them in there. The problem is, I've screwed the joists in through the 2x2 along the top already, so to screw the rafters down there I'm either going to be screwing into the screws that are already there or trying to screw into the edge of the plywood/trim. Should they maybe be offset somewhat from the joists and will that provide enough support for the roof?