Your Xantrex inverter/charger is the heart of the issue it seems. Note in your user manual:
http://www.xantrex.com/documents/Dis...ner_manual.pdf
That is says:
"NOTE: Freedom battery chargers are ON
whenever there is AC power connected to the
charger input, regardless of the condition of
the ON/OFF switch on the unit. The charger
can be controlled using the Freedom Remote
Control Panel or Link Instrumentation."
This is good, you want the charger function to be active when you have shore power. If it is not providing this, I recommend you read the manual a little more and ensure your Xantrex is setup properly.
As for charging from your engine alternator, there are several methods to accomplish this. Electronic modules (like a B.I.R.D.) or isolator solenoids, and then there's isolators that are simply two diodes in a finned case. Either way, you can replace your switch with one of these. My suggestion is to get a simple isolator (finned case with two diodes) and install it in place of the solenoid the switch controls. Might be the easiest (without seeing it that is).