Obx:
Here is a quick tutorial on marine DC systems. But you really should get a copy of Nigel Calder's or Charlie Wing's book on the subject.
Most boats as delivered from the factory have two batteries connected to a 1,2,all switch. The simplest way to use them is one for start and one for house loads. Use the switch depending on what you are doing.
The batteries are charged either by a shore power charger which is often separately wired to each battery independent of the switch and the engine's alternator which is usually wired to the start battery but can be paralleled to the house battery with the switch.
Gel cell batteries were first developed for aviation use as they can be mounted in any direction and don't require water to be added. But they have a special voltage profile for charging that is different from flooded cell lead acid (FLA) batteries- the ones that have been around forever.
AGMs were then developed which have all of the advantages of gels, but their voltage charging profile is close enough to FLAs that most, well some- me, don't worry about it. But they cost 3 times what FLAs cost.
8Ds were developed to start 8-12 liter 18 wheeler engines and boat builder's just went with the flow. But as I said on your other thread and others have said here, 8Ds are too damn heavy to wrestle around in a boat and a good group 31 will start any engine installed in what we call trawlers. You can use an FLA or an AGM in this service.
I am going to call it quits now and not get on my soap box about all of the so called deep cycle batteries sold for marine use and all of the various combiner, ACR, Echo Charger solutions out there. Read one of those books to find out more.
So, back to your specific questions. If your engine alternators are stock then it is highly likely that they are not right for gel cells. So I would not replace then with gel cells. I would replace them with two group 31 FLA batteries. Most are sealed anyway so you don't have to worry about adding water and will last a long time. So save your money and buy them from Sams, Costco or one of the other recommended suppliers.
You also have a shore powered charger that charges these batteries. Those built in the last 10-20 years have a selection switch for Gel, AGM, FLA. Set it to whatever you buy, hopefully FLAs.
To know how your boat is wired beyond the simple explanation above, you need to hire a good marine electrician to walk through it with you. He can quickly confirm my theory that your Cat alternators are not right for gel batteries and also help you to understand how to keep the house batteries from running down at anchor and taking your starting batteries with them.
David