I highly recommend buying the new 5/3/1 Forever book, it is going to have everything explained in great detail, along with several different programs to choose from. But to clarify:
Your Training Maxes will need to be 85% of your 1 rep max. Base all percentages off of your training max. Do not use your actual one rep max for calculating percentages.
LEADER (Cycles 1-2) (this will consist of two 3 week cycles)
Main work: 5s PRO (this signifies that you will do sets of 5 reps for all of the 5/3/1 main working sets. No PR set on the top set)
Supplemental work: FSL BBB (5 sets of 10 reps at the percentage of the first working set of the main work)
Assistance: 25-50 total reps per workout for push category, 25-50 total reps for pull, and 0-25 total reps for single leg/core work.
The main work and supplemental will look like this:
Week 1: 65% x 5, 75% x 5, 85% x 5; 5 x 10 at 65%
Week 2: 70% x 5, 80% x 5, 90% x 5; 5 x 10 at 70%
Week 3: 75% x 5, 85% x 5, 95% x 5; 5 x 10 at 75%
Now, increase training maxes by 5 lbs for bench/press and 10 lbs for squat/deadlift
Week 1: 65% x 5, 75% x 5, 85% x 5; 5 x 10 at 65%
Week 2: 70% x 5, 80% x 5, 90% x 5; 5 x 10 at 70%
Week 3: 75% x 5, 85% x 5, 95% x 5; 5 x 10 at 75%
This completes your Leader phase, once finished, use the 7th week protocol - Deload
ANCHOR (cycle 3 of the total program, do one anchor cycle)
Main work: 3/5/1 PR sets (PR sets on the first and third week, 5s PRO on the second week)
Supplemental work: FSL 5 x 5
Assistance: 50-100 total reps for each category
Week 1: 70% x 5, 80% x 5, 90% x 5+; 5 x 5 at 70%
Week 2: 65% x 5, 75% x 5, 85% x 5; 5 x 5 at 65%
Week 3: 75% x 5, 85% x 5, 95% x 5+; 5 x 5 at 75%
After completing this, perform the 7th Week protocol - Training Max test to test your TMs and make sure that they are correct to start your next program. The new book can answer any questions that you may have and has alot of great programs to choose from for getting bigger, faster, and stronger. Be sure to follow the guidelines that Jim has provided, he knows a thing or two.