Both shut the bike down. However using the kill switch still has systems powered up and on '08 TBW bikes that can cause problems. If you bump, twist or a fly farts on your throttle you can have your idle start to creep up over time. This can cause zero throttle position setting problems with power commanders. All your fuel settings can then get a little off from the throttle setting since 0 wasn't really zero.
Harley had computer flash "fixes" for this problem but then you gain throttle hesitation. If you have an '08 TBW bike let the idle settle down and shut off with the main switch. Every month or so do the reset procedure but turning off and on to make sure everything is reset.
Pain in the butt .... what do expect for a $25,000 bike??? I actually dumped the Powercommander and went with the Tmax for no more problems. The PC isn't the problem but it piggybacks on the crappy computer from Harley. Tmax all alone. Fuel Moto knows of the problem and tried to help me the best they could without fully giving up due to the junk Harley computer for TBW.
Good luck