Like they've all said, SQF is all about documentation. Take your pest control question for example: not only will you want to have the rodent traps at every entrance, but you'll want a map of your facility and the location marked of every trap. We utilize rodent bait stations outside only to minimize the risk of contamination, and every door has a tin cat trap on either side of it inside. In addition, we use pheromone sticky traps for 3 types of insects identified by our contracted pest control company, those are shown on the map as well, and they're located away from active production areas.
I've only been in food for 7 months now, and being involved during the first ever SQF audit of my company was my baptism of fire so to speak. What I learned from that experience was you are expected to defend your programs to the auditor, but your statements should be backed up in policy/program and training. It isn't enough to say "our custodian checks the pest traps." You need to have a procedure stating the frequency and how the traps are checked, then have supporting documentation that proves it was actually checked (once a week for us). It can be very overwhelming, but coming from AIB you probably have a leg up on most of these items. If your pest control is effective, documented, and poses no risk of contamination to your product, RUN WITH IT! Be proud of it, but be ready for your auditor to ask questions about it. If he has an observation during the audit (not a minor or major), tell him "Thanks, I'll take that under advisement."