Yes - you do the three categories regardless. I mention in the book that a HUGE part of assistance work is common sense and choosing exercises based on what you did/what you are going to do AND how you feel that day. So as long as you are smart about it, which isn't that hard to do, you'll be fine.
Yes, in general, I like FSL better than BBB. BBB is good but for long term improvement and recovery, it seems to fit better into a program. Remember that a program is different than a template. A program is looking a huge calendar; a template is looking a training week.
That's not to say BBB doesn't work, but you asked about doing 5x5, and using FSL work with 5's PRO allows for the intensity to wave from week to week with a light/medium/heavy week.