It's the total amount of reps done at the final set - so all the reps count.
We are also doing some cool things with blocks of time - doing things such as "as many sets of 3-5 reps in X amount of minutes" with FSL and the top set. It's the same kind of idea but we started playing around with this last summer and it's a fun way to train, provided you don't suffer from "I gotta be a bodybuilder" and do 100000000 things per workout. Also it is imperative that you notice bar speed - when that shits the bed, you have to do less reps, take more time between sets or cut out completely.
This has nothing to do with what you asked but it reminded me of that. Just remember that bar speed is critical.