You won't need a hot in run wire with most isolators, but they do come in 3 or 4 post designs, 4 post would use hot in run hookup.
Normal hook up would be to run the B+ wire to isolator, then one wire from isolator's labelled posts to their respective batteries.
Good look at wiring here: Dual Battery Setups
One of the EVAP purge valve wires will be hot when key is on, computer grounds other wire to activate valve, so remove connector to test which wire is hot with key on, and make sure it is off with key off, it is fused via the EEC relay power fuse, 30amp I believe.
Fuse 41 15amp, is just another key on source for 12v in engine compartment, not part of EVAP