Can the Alternator Charge Different Size Batteries at the Same Time?

Question:

My house batteries are two 6V deep cycle wired in line and my starter battery is a large 12V, both are FLAs. I usually start and run with both batteries on and at anchor switch to the house battery. A friend told me that I should not run with the alternator charging both batteries at the same time as they were not the same size. Is he correct? Should I start on one and then switch to house when running? I appreciate your response and your articles in PY. - John

Answer:

Thanks for the feedback about the PY articles, we enjoy writing them. Regarding your question, having battery banks of different sizes should NOT prevent you from having your battery switch on all/both when running the engine. Start your engine with the engine battery and after about 5 mins turn the battery switch to all/both so that both engine and house battery banks are recharged from the alternator. Once you get to a destination turn the battery switch to your house battery bank.