Seems like you have two problems,
a) low lights the night before (even tho connected to the pier and charger on)
b) GPS etc.. not engerizing from the 12v panel even tho engine is running; apparently the altenator is working because the batteries are getting a charge.
Since seldom in life does two things go wrong at once let's look for the simple solution.
A) your charger crapped out a1) your charger crapped out because your batteries crapped out or at least one of them did and maybe that boiled off the other
B) while farting around in the battery compartment you knocked loose or did not reconnect either the positive or negative cable that supplies power to your panel; or you reversed a connection (only takes a second) and blew the primary panel fuse.
There is no need to panic, it's not magic.
Alternatively, The more complex response:
While playing monopoly with the kids the lead horsie figure was loose and running around making random shorts in the system by creating lead horse droppings on connections, then it got hungry and ate some copper cable and caused opens in other places.
To fix that requires 4 bottles of rum, food for a week, 3 naked virgins (female, non-minors) and from 8 to 10 viagra's, PM me with my airline ticket reservations and I'll drop in and fix it.