It should work fine. Use one output from the charger for the house bank, and the other for the engine bank. Both house batteries will be locked in parallel, but That’s usually what you want anyway.
Also, you may want to relook you battery sizing. The group 24 battery should be perfectly adequate for starting the engine (it’s what Beneteau shipped stock on the 37 with 3YM30). Using 31’s for the house will give you ~210 amp hours of capacity, instead of just ~160 with 24’s. So if you have a need for the extra capacity and room for the slightly larger batteries that’s what I’d go with.
