I basically did the same thing as caddis. Here's a few rules I used:
All Instructor time was PIC. 90% or Primary and Secondary as an aircraft commander was PIC. Other time is other time--not in the seat. The rest is SIC. Most airlines also have conversions for military guys that allow you to add time (ex .2 per sortie or .02%). Check the info for the company you are applying with to make sure you know the conversion. Good luck!