Should I Run with the Alternator Charging Both Batteries at the Same Time If They Are Not the Same Size?

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.  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. - Jeff