The neck probably won't want to go all the was back in the pocket. If you set the neck so that the end of the tenon is touching the back of the neck pickup rout, then you probably won't be able to fit the neck pickup in the rout.

So put the neck pickup in place, then slide the neck in so the end of the fretboard is touching the pickup ring. I'd put some masking tape on the top of the body and mark off where the end of the neck goes, then you have a position mark for when you glue it in place. The pickup ring will probably want to sit about 0.5mm to 1mm on the neck side of the rout, just enough to hide the pickup rout from being seen.

You'll want a clamp on the neck tenon in the pickup rout, and one on the top of the fretboard.