The key point is that instrument time is logged "when operating the aircraft by sole reference to the flight instruments". Nice and easy.
Filing IFR simply determines by which RULES the flight is being conducted and does not reflect whether the flight is in IMC or VMC or whether the instruments were the sole means of operating the aircraft. You can of course fly in VMC whilst operating under IFR and still use your map.
Commercial aircraft are virtually impossible to fly to the accuracy required unless by sole use of the instruments.
Just as an aside, I only log instrument time for the sectors that I am PF. I guess this is standard practice though.
If you fly in the UK I would suggest using the CAA CAP407 logbook as it covers everything you could need and has very clear and concise instructions for each column.
Instrument flight " The column headed Instrument Flying is provided in order that flight time during which the holder manipulated the flying controls solely by reference to instruments, either under actual or properly simulated instrument flight conditions may be recorded. The time spent in practices in a ground trainer eg procedural trainer or flight simulator should NOT be recorded under Instrument Flying, but should be entered in the appropriate pages at the end of the log book."
Nuff said?