You can charge batteries of different capacities together, but you should not discharge them together, at least on a regular basis. I charge my 3XGp31 house bank along with my single Group 24 start battery, but always switch to house when we are settled for the night. Always. Knock on wood, but 19 years and counting.
I have a Balmar 90A alternator with a Balmar ARS-IV regulator, so I get 45-50 amps out of it at 1100 RPM and 85A at 2500 RPM. At least for a while. Last year I finally put a temp sensor on the alternator and now the regulator knocks it down to 35A when it gets too hot, so I end up with about a 60/40 charge ratio. Still gets me from 60% to 90% in an hour of motoring. Jim Watts Paradigm Shift C&C 35 Mk III Victoria, BC
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