The best advice I was given was to log to the most conservative requirements if using a single log book and the hours are to be used for licence or rating purposes in both systems.
When I did my FAA commercial, the examiner tired to trip me up by claiming that some of my night time did not meet the one hour after sunset requirements as they had been done in the UK.
Anticipating this sort of thing, I had printed off the sunset times for that lat /long for all the night flight.
After that he did not check anything else in the logbook and when I offered to show him my long cross country evidence (again done in the UK) he declined.
OK so I am a few hours short in night terms for JAR but does it matter?