Presuming one battery to start the engine, and one to operate the electronics. In that case there is nothing to think about; one starting battery, one deep cycle battery. If anyone tells you different, walk away. Heres why:<br /><br />You will want a true deep cycle to operate the electronics, not a dual use starting/deep cycle. The true deep cycle has thicker plates internally, and it can be used for starting in a pinch but they do not like to repeatedly dump the big amps in one quick chunk that a starting battery, with thinner plates is designed to do. If you really want to optimize battery-to-buck, you can use a pair of 6-volt deep cycle batteries (industrial or golf cart), wired in series for 12-volts. Also no problem using a pair of those 6-volt deep cycle batteries for the starting system. The 6-volters are ok with dumping the big amps.<br /><br />Suggestion: keep both batteries the same type, wet/wet, AGM/AGM or gel/gel. If you use a wet battery for starting, then use wet batteries for the electronics. This makes charging and maintaining a lot easier since they both use the same charging profile. Regardless of type, to maximize your batterys life, you should use a 3-stage charger that utilizes a bulk/acceptance/float charging scheme. Wet batteries cost less and you have the advantage of being able to equalize the cells, should you choose to do so, at a higher voltage than is possible with gel or AGM batteries.<br /><br />As far as brand names, it will depend on your demands on the battery. Little demand, cheap battery. Big demand, not cheap battery. The deeper the discharge beyond about 10% of the rated A/hr, the less cycles you will get from the battery. One thing that is true with batteries in general, is you get a disproportionably bigger bang for your buck with the more buck you put out. This is especially true with the deep cycle batteries. A $100 battery may recycle 700 times to 50% capacity. A $200 battery may recycle 2100 times to 50% capacity or 1600 times to 80% capacity.<br /><br />Brand names: probably the best deep cycle battery you can buy is the Concorde. It was designed for use in the militarys stealth aircraft. It also sees a lot of use in home solar systems, where a lot of regular, daily deep, deep cycling is expected. Next to that is the Surrette (a.k.a. Rolls in America). It is a great battery. They retail for about ¼ list price, but still cost more than most other batteries. The Deka made by East Penn Mfg. is a kick-butt critter. It is a high discharge AGM battery.<br /><br />For a starting battery, middle of the road is a good place to be. If you keep the engine maintained, you reduce how deep the starting battery needs to go to get things done. They do not like to go down far at all. Exide batteries are very common as a marine starting battery, and affordable. Actually, compared to the cost of a deep cycle battery, any starting battery seems affordable. 
<br /><br />In this case, size does matter. The discharge profile affects the available capacity. The faster you discharge, the less your battery is willing to give up, or the less capacity the battery can offer. If you have a big demand over a short period of time, you get less capacity. This means the juice you sucked out of the battery was a bigger percentage of the now (reduced) capacity, which means your battery went down deeper, which means you get less cycles out of the batterywhich means less battery life. Except for high-end batteries, deep cycle batteries should not be discharged below 50% of their rated capacity. Concorde and Surrette/Rolls (and a few others) can go down to 80%. Whatever is on your boat put the same group size (or 1 size bigger) back, unless you know there was a problem that requires changing a bigger battery. There will be no harm in bumping up the deep cycle. You can only benefit, up to the point where you are trying to install a 4000-lb battery. If you have a group 24, bump to a group 27. If group 27, go to group 31. Depending on how you use your cruiser, you may be a candidate for a group 4D deep cycle house battery.<br /><br />My current project involves two 24-volt systems. I do not like the gel batterys deep cycling/charging profile, and AGM doesnt equalized like a wet so all batteries are wet. Eight 350 a/hr Dekas came out. The starting system will be a pair of Exide group 31s. I would like to use group 4Ds but weight in the new location is an issue. The house system is four Surrette 6-volt industrial batteries, equivalent to 16Ls. The group 31s are considered bare minimum to turn over a cat diesel, but I have the ability to bridge the two systems to allow using all those 6-volter as a giant starting battery too, if ever needed. You should install such a switch, too. You never want to bridge the two systems unless it is needed to start the engine(s). Never bridge the batteries for charging.<br /><br />If you end up with wet batteries, there is something called a hydo-cap that you can put on them. All batteries, especially wet cells, off gas. They change H2O into H and O2. That gas escapes through the cap vents. What a hydro-cap does is put the two gasses back together and water drips back into the battery. They are designed to drastically reduce the fluid loss from batteries. I have not used the hydro-caps, but the technical folks at Surrette highly recommended them to me. They are not cheap. Different manufacturers make these caps under varying names.
<br /><br />In this case, size does matter. The discharge profile affects the available capacity. The faster you discharge, the less your battery is willing to give up, or the less capacity the battery can offer. If you have a big demand over a short period of time, you get less capacity. This means the juice you sucked out of the battery was a bigger percentage of the now (reduced) capacity, which means your battery went down deeper, which means you get less cycles out of the batterywhich means less battery life. Except for high-end batteries, deep cycle batteries should not be discharged below 50% of their rated capacity. Concorde and Surrette/Rolls (and a few others) can go down to 80%. Whatever is on your boat put the same group size (or 1 size bigger) back, unless you know there was a problem that requires changing a bigger battery. There will be no harm in bumping up the deep cycle. You can only benefit, up to the point where you are trying to install a 4000-lb battery. If you have a group 24, bump to a group 27. If group 27, go to group 31. Depending on how you use your cruiser, you may be a candidate for a group 4D deep cycle house battery.<br /><br />My current project involves two 24-volt systems. I do not like the gel batterys deep cycling/charging profile, and AGM doesnt equalized like a wet so all batteries are wet. Eight 350 a/hr Dekas came out. The starting system will be a pair of Exide group 31s. I would like to use group 4Ds but weight in the new location is an issue. The house system is four Surrette 6-volt industrial batteries, equivalent to 16Ls. The group 31s are considered bare minimum to turn over a cat diesel, but I have the ability to bridge the two systems to allow using all those 6-volter as a giant starting battery too, if ever needed. You should install such a switch, too. You never want to bridge the two systems unless it is needed to start the engine(s). Never bridge the batteries for charging.<br /><br />If you end up with wet batteries, there is something called a hydo-cap that you can put on them. All batteries, especially wet cells, off gas. They change H2O into H and O2. That gas escapes through the cap vents. What a hydro-cap does is put the two gasses back together and water drips back into the battery. They are designed to drastically reduce the fluid loss from batteries. I have not used the hydro-caps, but the technical folks at Surrette highly recommended them to me. They are not cheap. Different manufacturers make these caps under varying names.
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