A starting battery for each engine is a great idea. I believe that the best batteries for this are Optima spiral cell AGM batteries, they are expensive but I bought mine in '2000 and they are still going strong.
There is a lot to be said for completely separate starting circuits for each engine, but I have set mine up with two explosion-proof battery switches so that I can connect either battery to either engine, or both batteries to one engine, if needed. Some folks prefer to keep short jumper cables handy for emergencies, but watch out for sparks.
I have a third battery switch for the two house batteries, so that I can run the boat on either or both of them. The idea was that I could drain one and still have the other. I now think that this is too complicated, one large AGM battery should do the trick. I have a pair of 75 A-hr Optimas, and they are good for three days at anchor. Try to reduce power use to keep the size of this battery down (LED lights, etc.)
I use a 65-watt solar cell to provide a trickle charge to the starting batteries. Even if dock power fails and everything goes flat, I can start. I use a 15A dual-output float charger for the house batteries.
I charge all batteries simultaneously using a diode splitter that I built myself. Doing it again, I would buy a couple of those combiners that connect the batteries automatically when one is being charged. I would also get a multistage charger for the house batteries, a little bigger than the 15A I have now.
You can see the way I have wired my boat at
www.geocities.com/dougmrose
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida