Yeah, pretty much.
Leave the battery cables hooked up to the switch like they are now, heavy guage wire, 2 guage or better (numerically lower is larger).
Then all you need to do is run the charge wire from the alternator (the stud) to the "alt" post on the isolator, then from each battery go to the two "bat." studs on the isolator, one each obviously.
Then when you run the boat just make sure the battery switch stays in the #1 position.
To double check your wiring, just remoe one negative battery post at a time and see what's powered up.
Hopfully you don't have an ammeter, because these are a horrible way to go IMO, the charge circut would need to run from the alt. to the ammeter, back to the isolator then to each battery, thats like 40 uneccissary feet of wire at 30-60 amps., a little dangerous IMO again...Use a voltmeter.
Make sure you have a large ground wire to each battery to the engine block, and a large positive from each battery to #1 and #2 on the switch. I will try to draw a diagram at lunch but should be pretty straight forward.
As always good luck.
TTFN
GT