I save whenever I want.... ususally just before something grand is about to happpen..... like nailing that big fat juicy convoy that just appeared out of the fog. LOL Or supper, or whenever the Warden calls.
I do the written log too. Helps keep track of the good Grids to catch the enemy in.
If you do not try and install a mod during a patrol you shouldn't have problems saving anytime you want during a patrol, unless you have sound issues or some other problem not related to SHIII.
Only install mods while "In Base". Installing mods during a patrol will cause you to lose your campaign, unless you have it all backed up and safe.