On my consolidation spreadsheet, I had two columns. One was labeled "Part 61 PIC" and the other was labeled "Military PIC". I had Marine, Air Force and civilian flying over my career. For the military stuff I put all my Aircraft commander time in the "Military PIC" column; that was cut and dry. On dual sorties where both of the guys in the cockpit were equally qualified, I put the time where I was sole manipulator of the controls into the Part 61 column.
The important (really important) part is to give the hiring department what they ask for. If they specifically say they want only the time where you were signing for the aircraft then do NOT include the part 61 time. Like the other guy mentioned earlier, most companies do NOT want part 61 time.