Ok a few things here to look at and think about.
The least resistance and more surface are you have for your electrical to run through the better your performance will be. A couple more power and ground runs will not hurt you in any way.
Always good to check out your equipment and make sure it is running the way it should be. In this case the batteries and alternator would be the first places to check. From the way it sounds all three are working the way they currently are designed to operate. If you want to get them checked out, then you can always go by an auto parts store (pepboys, autozone, advanced, etc...) and they can test everything for you. The thing to remember when doing this though is that you need your batteries fully charged before they run the tests, and some of the people running the tests at these places know less about how to actually test a battery than my 12 year old daughter does. It is an option though. They can also check your alt for you as well.
I was going to tell you about the tow mode, but looks like you found that out.
From what you have posted I think your batteries are probably ok, but they probably are not getting topped off with a charger. Remember alternators are not designed to fully charge your batteries like a charger will. Especially if you are playing your system running the batteries down most of the time when you are driving. Investing in a few more power and ground runs along with maybe an AGM battery charger will fix part of your problems, but the biggest issue you currently have is the PCM control on the vehicle.
If you upgrade your stock grounds and you see that one of the factory grounds has a sensor around it MAKE SURE you keep that ground exactly the same. If you delete that sensor it can really screw you up.