Chances are you are not rigged right. Many boat mfrs get lazy and don't rig to ABYC standards - the organization that sets standard for boat building and rigging. Without quoting their scripture verbatim, it translates to::
Each and every engine should have it's own dedicated battery. Nothing else on this battery except the engine stuff - so for us thats DTS , power steering and smartcraft devices. And then adding a separate battery (or more) for everything else on the boat - baitwells, stereos, lights, etc. This is called the HOUSE BATTERY.After messing with this for a few years, we now recommend a BEP BATTERY CLUSTER. This will replace your big red batt switches you probably now have. Blue Seas also makes some good devices, but this one is simpler and more all inclusive. Your mfr may have a diff way of doing it, and that's fine as long as you have a house battery setup that gets charged. This is a product that will:
1. allow you to charge all your batts from a shore charger or the engines
2. if you drain your house batt, it will leave your engine batteries charged and intact
3. allow for emergency starts using the other batts if one goes flat.
4. work just like your big batt switches now in that you can turn everything off for storage
This module is easy to install and incorporates all the features/advantages you may read about, "isolators", "combiners", "ACR"s or "VSR's". Here is one for a single verado, using two batts - requires no extra cables - just replace your batt switch:
Click here for a slideshow of an install by our expert TomThey can be found here. If you need expert help, call BEP for technical assistance:
CLICK HERE FOR THE BEP LINKBecause this is a technical discussion and it's important you do it right, please call BEP to proceed. They are great to work with. This thread is locked and you cannot post questions here.
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That being said, there is an easier way for simple situations (day and lake boaters, etc) :There is an easier way for guys with single V's on lakes and such. You just need more reserve capacity. Just add a battery in parallel (pos to pos, neg to neg) with what you have now. Add a simple on/off batt switch on the positive cable between the batts. Put all your loads that drain a batt when you fish or party: baitwell, stereo, lights, etc. on this batt with a fuse block. Put the switch "on" when you leave the dock so the batt charges when running along with the engine batt. If you stop to fish or party, click the batt switch "off" so they are separated. When you start back up, click it "on" so it charges again. Doing it this way, you are a "manual combiner/isolator" yourself. The downside to this system is if you forget your "on and off" responsibilities, then you could be dead in the water - literally.
This involves buying 3 short batt cables, a simple on/off batt switch like this:

and a batt box/tray. Buy the same batt you have now - don't mix models and types. Make it a bulletproof system by replacing all your batts with Sears or Odyssey AGM.
Get a yard to help you if you feel uncomfortable doing this. For legal reasons, we cannot go any farther here.