Hi David,
to be honest I've never bothered about which fan is which but I always thought the System Fan was the one on the back of the chassis as in earlier PC's this was the only fan installed.
Yes, if you are running directly from the PSU power connector you will be quite safe using a split lead. One thing to note though, is that the fans will always run at full speed, not a bad thing in my opinion, but if you wanted to control their speed you won't be able to with this method.
I have a Noctua CPU cooler and I actually run this directly from the PSU too, rather than the Mobo headers, as the fans don't respond well to the variable voltage. Not everyone's choice I know, but it does mean the cooler fans are working from the minute I switch on the PC and I never have CPU temps higher than about 35°C.