Your strategy depends on what you need to accomplish with the files. I.e. maybe they are needed if you are into e-racing and have to provide the second, independently recorded file.
I use my indoor rides purely as training but nevertheless always record double. In my case one file is the Trainerroad .fit file from their app. Showing the wattage from the smart trainer, a distance column (as proxy from the used gearing) and my heart rate sensor.
My single source of truth is the file I record with my Wahoo, which reads the same heart rate monitor but the watts (and cadence as well as l/r balance etc.) from my Powertap P1 Pedals.
Only the latter is stored in GoldenCheetah and also only these fit files are additionally stored in a separate folder (just for archiving purposes). I like to copy over the distance column from the Trainerroad .fit files - just so I can use this number in addition to total training time to have an appropriate glance over volume). And from time to time I overlay the curves of watts to check reading differences in various watt ranges. But I then routinely delete these Smarttrainer originating files. They are of no further use for me.