If you use an isolator, you must make sure it's not the cheap diode type. I used a Hellroaring isolator on my old boat, it is a sophisticated, solid state relay based isolator. You can also use a Stinger continuous duty relay to disconnect, that's the second best alternative.
I'll sell it for 50$ if you want it, works fine. I haven't got around to putting in a second battery in my new boat and probably won't. I would put the second battery near the load, if it's a second starting battery put it not too far from the old one. If it's for a stereo or accessories, place it near the amps. The charge wire can be long without problems but long 00 gauge wire is very expensive. I used the BIC-75150A.
http://www.hellroaring.com/bic75150.php
