Kitten do you mean the snaps fitted to the booster touching bub or the snap sockets where the booster would snap in if you dont have one there?
You would only need to use one booster and attach it to the back snaps. You won't be able to use the front snaps on the small setting as the front flap will be folded over!
A fleece liner would cover the snap caps on the booster enough that it wouldn't be uncomfortable.

I hope I understood your question properly