I'm building a neck through fretless bass and what I have so far is the neck blank with the neck rough cut but not shaped. When it comes time to cut down the part of the body where it gets shallower after the fretboard ends I'm worried about how far down to cut it. I want to be able to have really low action. I already have the bridge so should I do measurements with the bridge?

If the bridge can be raised to a height that will cover for the max height you can imagine wanting in the near future, you cut to have the bridge in level with the board, when in lowest position.
You could also consider a neck angle.

I'd suggest you look through this forum for book suggestions, and get a book, so you can plan this properly. Without proper advance work, you'll likely end up with problems. The Melvyn Hiscock book is a good one, and there are others.