Isolators are not all that great, you will lose about a volt across one. Wich means that your alternator is putting out 13.5 to 13.9 volts to charge your 12 volt battery to 12.8 volts. Given tose standards it is pretty hard to get a full charge at 12.5 to 12.9 volts under normal circumstances. The best compromise may be a 3 position battery switch. Leave it on both while the alternator is charging and if you plan on a load for awhile with out running the alternator then switch batteries accordingly. I will be going to 2 golf cart 6 volts in series for my deep cycle bank ( house batteries), and keeping my starting battery just in case. the two six volts are replacing my single deep cycle only because we overnite on the anchor occasinaly and I want an inverter to make coffee with...other than that I have had great luck with one deep and one starting battery on a three position switch. This is by far not you only option. And if you think you might forget and leave the battery switch on both when you shouldn't then this set up definitly is not for you...

Buy the 12 volt bible...or 12 volt boaters bible...its out in my boat right now and I am not going to go get it... ..
It addresses all of these questions and gives you solid answers and explanations for those answers. And it is not some huge 3,000 page tome you cannot find anything in. Its a couple hundred pages, very easy to understand common sense. You will not regret this book...mine spends more time loaned than it does with me!
I am sure Amazon has it and I know BW and WM both stock it