You didn't say what branch of service you were in, but in the hard cover logbooks used by the USN and USMC, there are 4 columns under the header "PILOT TIME". Those 4 columns are listed below, along with a brief explanation of what I remember we would log in each category:
- TOTAL PILOT TIME - (The sum of the other three columns - note that it isn't called total "FLIGHT" time...)
- FIRST PILOT - (Time logged as manipulator of the controls.)
- CO-PILOT - (Time spent not as manipulator of the controls, but may be acting as navigator, talking on radios, instructor letting student fly, etc.)
- A/C COMMANDER - (Self explanatory, similar to PIC in that you can act as A/C commander even while not manipulating the controls, so time in this column may or may not match either of the other two columns.)
These categories are roughly equivalent to FAA definitions of PIC and SIC time, but they obviously aren't an exact match. Clearly though, total time is ONLY intended to include pilot time.
There is a separate column, NOT under the "pilot time" header, labeled SPECIAL CREW TIME. This column was used to log time for other crew members such as non-pilot rated officers, (Naval Flight Officers) or enlisted crewmembers such as flight engineers and loadmasters. It could also be used by rated pilots in case they wanted to log total time in the airframe while not occupying a pilot seat or performing pilot duties. (such as dead heading in a back seat) Many of my pilot friends purposefully avoided logging crew time to keep their logbooks "pure".
Since you cannot log pilot time when not occupying a pilot seat, and since there is no category for total flight time, the question really becomes, what is your operations officer wanting to do with "TOTAL" time?
Because if you stick with the way the logbook is laid out, then total time will only include pilot time. If you want to track special crew time for any reason, then log it. It probably won't count for pilot upgrade purposes, (depending on policy) but it might be good enough for your local Lockheed Martin representative to present a 1000 hour pin.
However, if you want to somehow differentiate between reading/sleeping in the cargo bay on long flights vs sitting in the flight engineer seat observing and actively participating in quality training, (which has tremendous value, and I think is really the root of your question...) then establish a policy to only log crew time when directly observing the two pilot seat occupants.
Alternately, you could choose to log all non-pilot "flight time" in the airframe time as crew time, but create a separate training spreadsheet to track non-pilot seat, active monitoring of the PIC and SIC, with the A/C Commander signing off the training log after each flight.