The ONLY way that I would consider mixing AGM and Wet-Cell batteries, of different ages, is with the HOUSE bank as AGMs, and the START battery connected via an Echo-Charge. I would verify that the voltage regulator is capable of working with AGMs, and that your alternator is up to the task of charging the house bank. The battery switch would be switched to the start bank to start, and then quickly switched to the house bank at any time when the engine is running.
In general, my learning from the posts in SailNet, and elsewhere, is that one should not mix battery types. YMMV
AGMs do not need to be kept in a box, they only need to be secured.
Good article here: Pacific Power Batteries - About Automotive Batteries
AGM Pro's: better cycling and depth of dischager over the wet or gell batteries. While most wet batteries are supposed to only go to about 50% depth of discharge, the AGM's are able to go to about 20% depth of discharge without harming them PROVIDED that you don't overcharge them at too high a voltage on their return.
This is what is so frustrating about the internet, that poor information, is trumpeted as truth..
That data was EXACTLY how AGM batteries marketed and launched themselves into the marine market. Those bogus promises of longer cycle life and more usable capacity than deep cycle flooded batteries was soon ousted as a mistruth in the "real world" where the battery life really matters.. These misleading marketing attempts really bit them in the ARSE because cycle life at 80% DOD SUCKED....
Today nearly every maker of AGM batteries, Lifeline, Deka/East Penn (and all their private labels), Trojan, Rolls etc. etc. all recommend a 50% DOD not 80% DOD.
Odyssey still sells on 80% DOD but they readily admit that at 80% DOD you only get 400 cycles.
(and this in in a laboratory with white glove treatment)
At 80% DOD with a flooded group 31 Rolls 12V battery you get 800 cycles or DOUBLE the life of an Odyssey AGM at 80% DOD. DOUBLE the rated cycles !!!! The Rolls battery also costs less than HALF of what an Odyssey does.
With a Deka/East Penn AGM group 31 12V battery you get 250 cycles to 80% DOD.
Compare that to a US Battery DCXC group 31 flooded deep cycle battery that sells for about $120.00 and it gives you 675 cycles at 80% DOD!! Bump that up to 50% DOD and you get 1150 cycles yet the Odyssey only gives 700 at 50% and the Deka/East Penn 500 cycles at 50% DOD..
Oh and to even attempt to come close to 400 cycles at 80% DOD with Odyssey batteries you need a minimum of 40% of capacity in charging current. So a 400Ah bank needs a charge source capable of maintaining 160A. If this is an alternator you'd need a cold rating of about 200A to have 160A when hot.... How many boaters can do that or expend all that money just to hope they "might" get 400 cycles when a cheap $120.00 battery will give 675 cycles with no fancy charging system upgrades.....
The fact is that AGM's do not offer longer life or deeper cycling an this has been priven time and time again in the "real world" and also in the lab by the manufacturers.. The manufacturers own data shows shows this, it's where I got the numbers from above.
I find this to be an interesting quote by Trojan Battery. When AGM's first came out the claims were BETTER cycle life than wets as that web site still seems to claim..
Originally Posted by Trojan Battery
Generally, gel and AGM batteries have about 20% less capacity, cost about two times more, and have a shorter cycle life than comparable flooded lead acid batteries. However, Gel and AGM batteries do not need watering, are safer (no acid spilling out), can be placed in a variety of positions, have a slower self-discharge characteristic, and are more efficient in charging and discharging than flooded batteries (see table below). Gel batteries are more suitable for deep cycling applications whereas AGM batteries are more for light cycling and engine-starting applications.
Keep in mind that ALL of those numbers are LAB DERIVED where temperature, charge rate and charge/discharge cycles are done very methodically and repeatably. Those numbers are NOT at all indicative of what you'll see in the real world. If you want real world numbers chop 50% right off the top and now you're in the ball park..