on my old '87 Firebird Formula, i had the e-fans set up to use a factory-style thermo switch and only had another switch as an override...i think that is the safest way to wire 'em up. for a little bit, i didn't have the thermo switch and i remember a few times on the way to work i almost burnt up that poor lil TPI 305...
I have a switch as an override just in case my controller stops working. I drilled a hole in the center consol right next to the cigarette lighter and put a toggle switch in there to a relay. I can still keep my change in the ash tray and the lighter is still accessable. It's tucked away and really easy to get to. I used 10 or 12 gauge wire btw.
Kevin