I have a 2001 Beetle and had similar problems.
The Dealer told me when the car is not in use to use the remote and lock the doors.
This shuts ALL electrical devices off.
Another problem could be a light left on that you can't see like in the trunk or glove box.
Yes the boat will still need a battery. The alternator is used to recharge the batteries. So when the batteries are ran down by starting it or using the troll motor, the alternator only charges them back up so you don't have to.
Start the truck then disconnect the battery if it's still running the alternator is good
the battery job is to start the car so the alternator will kick in after the car is running
Check for fuel and spark to the cylinders
If the alternator is bad the car will still start. You just need a fully charged battery. Once running then you can check the charge rate from the battery with a volt meter.
That could be the alternator or the battery. Try jump starting your car with another car's battery. If it still does not start, it is probably the alternator. If it starts, your battery is dead.
Cold does that to car batteries and (some) engines. You might consider replacing the battery, or if the battery is still fairly new, consider having the alternator and charge relay checked out.
possible weak batteries?
A quick test I've always used is to start the car. Remove the neutral cable from the battery. If the car still runs your alternator is fine.
If the engine turns over the batteries are fine. Diesels require special equipment to troubleshoot, take it to a shop that is competent in diesel engines.
The problem isn't your batter or alternator or starter then. Start looking into your fuel management system. Possibly your fuel pump, injectors, etc.
Sometimes, brand new batteries need to be charged for a while before they have the power to engage the solenoid/starter properly. The battery may have enough jucie to light up the headlights and run the stereo, but not to crank the engine.