Total Time=Pilot Time, but log Flight Time
14CFR 1.1
Flight time means:
(1) Pilot time that commences when an aircraft moves under its own power for the purpose of flight and ends when the aircraft comes to rest after landing; or
(2) For a glider without self-launch capability, pilot time that commences when the glider is towed for the purpose of flight and ends when the glider comes to rest after landing.
61.19(b)(12)
Pilot time means that time in which a person--
(i) Serves as a required pilot flight crewmember;
(ii) Receives training from an authorized instructor in an aircraft, flight simulator, or flight training device; or
(iii) Gives training as an authorized instructor in an aircraft, flight simulator, or flight training device.
Interestingly, although "total time" is not defined in the FARs, in 61.159 "total time" refers to pilot time. If someone asks how much total time you have, you can include sim/ftd time. If they ask how much flight time you have, do not include sim/ftd time.
For meeting the aeronautical experience requirements for an ATP certificate, you need "1500 hours of total time as a pilot", which is pilot time and includes simulator or FTD time. For a commercial certificate under part 61, you need "250 hours of flight time as a pilot", and that flight time does not include simulator or FTD time. Also to meet the PIC requirements for 135.243, sim and FTD do not count toward the flight time requirements of 1200 hours (or 500 for VFR operations).
Pilot time includes instruction given or received in a simulator or FTD. Flight time does not include any simulator time. If your logbook column says "Total Duration of Flight" or otherwise uses the word flight, do not include sim time. Most logbooks have one "Total Time" column, so to be consistent between logbooks, only log SIM & FTD under SIM/FTD, and log the approaches. Do not log landings, multi-engine time, simulated instrument, cross-country etc. To calculate your "Pilot time", just add the flight time and Sim/FTD time. You want the instrument time seperate because there is a limit on how much SIM/FTD time you can count towards experience requirements, and also you want to know how much instrument time you actually have in real airplanes. To calculate the total instrument time, just add SIM/FTD to actual and simulated instrument flight time.
So log FLIGHT TIME in your logbook, but total time=pilot time and includes SIM/FTD. If you logged TT in your logbook (including SIM/FTD), no biggie, just be consistent and subtract SIM/FTD from TT to get flight time. If you change to a logbook that has "Total duration of FLIGHT" etc., carry forward only the flight time and make a note of it. As long as you are consistent and accurately report your flight time, I don't think you are going to have major problems.