Mark,
these are a v. good on boat charger that we have used in dual and triple batt instals.
http://www.dualpro.com/
They are a bit on the heavy side but in a bigger boat it is not an issue.
As for batt. type you will get a bunch of diff answers. We sell about 60 batteries each year. AGM we use LifeLine. Wet I like Trojan, Deka, and we have had good service from Interstate Marine line. Die Hard works too. Top is Rolls but all these need water added and can not be used on their sides. Only a couple of lead smelters left so most batteries come from the same place with box and label sold to each OEM. We are testing the Odyssey Battery in some boats, but they have been described as Alternator killers due to unbelievable low internal resistance. The regulation of the alternator never sees any resistance and just keeps hammering away(Equals massive Heat for the charge system)
If you keep the cable runs down you will be OK with the electronics on the start bat. The Troll batt will get discharged most likely and will not always be there for you to navigate. Some guys go with a mini motorcycle batt to power the GPS so it dosnt fall out when starting off the Start Batt.
If you like to read, Blue Seas has some very good stuff for charging, circuit protection, and switching.
http://bluesea.com/category/2/productline/overview/329
Also their wire size calculator is invaluable for getting the right size battery cable for the amperage you expect to use.
http://beta.circuitwizard.bluesea.com/
This may be more than you want to get into and can be done manually with a 1,Both,2 switch but Im not sure how much you are into the electrical layout of marine stuff.
If you have questions let me know.