Hi Phil,
I am also of the flooded battery camp. They have the best value. AGM are good if you need/desire their advantages such as no watering maintenance, lower self discharge rate, and lower internal resistance. I used an AGM battery in my airplane. Due to the very small battery size (25AH!) that needed to start a 320 cubic inch engine the AGM provided better starting performance. The lower self discharge also allowed the battery to hold its charge better during 1-2 week idle periods. If you do go with AGM get a good one such as the LifeLine. They are made by Concorde which made the aircraft battery that I used, this is a highly regarded company. I woyuld not recommend the Optima, it uses a spiral cell design which wastes space and reduces capacity.
I permanently connected the thruster and house banks together in my R27. This was a double win, the house bank is 50% bigger and the thrusters actually work better with 3 batteries in parallel. I did a rewire project adding 600A bus bars and a Victron battery monitor. If you do something like this make sure you use the correct battery cable, lugs, heat shrink, and crimping tool. Photos are in my album.
I will be starting my 4th season with the factory original Centennial batteries. They were still working well at the end of last season. They have been in the boat over the winter on the hard at the marina. I disconnected them and they still were at about 12.7V last weekend. I reconnected them and powered up the battery chargers to top them off (I have added a 45A auxiliary charger to supplement the factory 20A charger) to top them up.
Warehouse clubs are also a good source, the marine deep cycle batteries in Sams Club, Costco, etc. are made by either East Penn or Johnson Controls, both good companies. These are a good value. When I need to replace my batteries I will go to Sams club. Try to avoid the dual purpose batteries if possible for your house bank, you want a good deep cycle battery to provide longer life. The engine battery should be a starting type.
Howard