I'd offer that one deep cycle and one starting is the best way to go for batteries, but the best way to keep them happy is with solar to keep them charged up. A battery will, over time, and for some thoroughly technical reasons that I'll gladly leave for those that like that kind of stuff, lose their ability to maintain a "full" charge.
The deep cycle battery, used for house and electronics, should never be allowed to fall below 50% of it's rating, as doing so will prevent the battery from coming back to 100% charge. It may only come back to 99.5%, but next time it's run down into the ground, it may only come back to 99.5% of the 99.5% that it started from and so on. It may seem tiny, but do this every weekend and suddenly a three year warranty on a battery is being exercised well before it should be, and your time is worth something, driving around looking for a replacement when you could be boating.....
A deep cycle battery is intended to provide a steady supply of current for a long time, while a starting battery is intended to supply a jolt of current, right now, to get the 'ol diesel spinning.
A dual charge controller (We have a SunSaver Duo) allows a single input to connect to two batteries, and the charge controller is capable of dealing with each battery separately.
I'll go on record as telling that we had an 11 watt panel on our M26c, a single battery, with an older style charge controller, and I got 7 years out of that battery. I believe that is the exception, rather than the rule. A good charge controller and a 15 watt panel is quite possibly enough to keep both batteries fully charged, if you use it to "top up" the batteries, and not as a primary source of your needs. Of course a 15 watt panel will not run a boat full of toys, air conditioning and 2 fridges, but there's more than enough sun through the week to keep the batteries charged up for next weekend.
If your bilge pump is wired directly to a battery, the panel switch should be in the "off" position when you're not there.
The "best" battery? The one that costs $59.00 for 750AH, and comes with a 5 year warranty. If you find that, let me know! Local availability may vary....
Cheers
Gary