My guess is that you are slowly running them down. I don't know what size batteries you have, but lets say they are a pair of 100AH group 27s. If you run them down to 60% state of charge by hanging out at anchor with the fridge and stereo on for a few hours, you have to make up 80 amp hours of charging to bring them up to 100%. Lets say your OEM Mercruiser alternator produces 70 amps max (probably 50 amps at cruising speed). The fridge and stereo probably stay on while you are underway, so there's at least 10 amps used, the engine probably absorbs another 10 amps to run, now you have 30 amps to spare for charging. If everything was perfect and batteries charged at 100% efficiency all the way to 100% state of charge, you would need to cruise for 2 hours and 40 minutes to recharge the batteries. However, the batteries will not charge at 100% efficiency and after 2 hours and 40 minutes, they won't even be to 90% charged. Realistically, who's really going to drive around on plane for nearly 3 hours after a day spent anchored? A bigger alternator would help and AGM batteries are a better choice then flooded lead acid (they charge more efficiently than flooded lead acid) but the best solution with what you have now is something you already know, you need to charge them while the boat is parked.
Another solution would be to use a Lithium Iron Phosphate (LFP) battery for house (everything but engine starting and running) loads. Install a Blue Sea Systems ML ACR that is connected to prioritize the starting battery first and a single 100AH LFP and you will have vastly improved your situation. One big caveat though is that the LFP cannot reside in the engine space, they cannot handle the heat, so it will need to be moved somewhere cooler. LFPs recharge at about 99% efficiency from dead to 100% SOC and they are not bothered by being stored partially charged. Another caveat is that the LFP should never be used to start the engine, so you lose a some redundancy but if you never run house loads from the start battery, it'll always be fresh.
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