If you mean the 5/3/1 sets for your main movements, you do the prescribed reps and shoot for a PR. You determine your goal for the last set based on your estimated 1RM (Weight x Reps x 0.0333 + Weight) & previous PRs.
Compound variations of the main lifts are supplemental work, not assistance. I suggest you read Dave Tate's take on it:
For programming assistance:
And most importantly, read the books. Sorry if this post appears twice, I tried to edit it once and some parts disappeared so I did it again.