Cameron,
You "log" your military hours as military hours.
The next issue is how you might report or "slice 'n' dice" those hours to various people like the FAA and potential employers.
For the FAA, you can use a combination of the "sole manipulator of the controls" definition in FAR 61.51.(e)(1)(i) the "pilot in command of an aircraft on which more than one pilot is required" definition of 61.51.(e)(1)(ii) to total your "PIC" hours. If you were not an Aircraft Commander, only your "Primary" time counts as PIC, but your "Secondary" time counts as SIC time.
For job application purposes, each airline has its own definition. Many count PIC time ONLY as that time during which you were the designated Aircraft Commander, regardless of "manipulation of controls." Others will allow any "Primary" time to be counted. You have to read each application carefully, and be prepared to justify your answers in the interview.