Hi
While logging training for your FAA IR, the FAA rules allow you to log the time as PIC. I would have thought your instructor would have explained this as I was surprised when my instructor made me log my hours as PIC on doing theFAA IR.
This is unlike JAA where you would have logged the hours as Pu/t.
If you were logging time as a safety pilot, then you would log only the part of the flight that you was responsible for being the PIC of that flight. ie the time YOU were looking out of the window and the other pilot was flying on instruments. It needs to be clear at the start of the flight who would be logging what time in there logbooks.
Hope this helps.