We did not use the checklist until this year. We chose to start using it because in Edition 9 they are requiring supporting comments on each clause, just like the SQF Auditors have to do. We found it was much simpler just to use the checklist provided by SQF because it is designed for that and you know everything is included so you won't miss anything. We maintain it electronically on a shared file.
We chose to divide the checklist out by sections and we do 4 to 5 sections each month. I am fortunate to have some great co-workers so we have a multi-disciplinary Internal Audit Team and split the work between us. I just have to provide annual training on Internal Auditing for them. It is a win-win-win because it lessens the work load, they understand more of the behind the scenes requirements, and it helps to support our food safety culture (another updated section for Edition 9). - I do like the concept of going through the checklist all at once. It would take some coordination of schedules since we use a team but I appreciate the idea being shared.
Like Spidey, we have a separate Monthly Internal Audit for GMP's in addition to the SQF Internal Audits and the Internal Audit Team covers those as well.