Dave:

If you connect the two batteries with no charging with your
manual switch, the battery with the higher charge will start
bringing the other battery up, as it goes down, until they
are equal.  With charging, the "full" battery will take a
little charge, since there is a float voltage that can always
be applied to a battery and the other battery will get a
charge, and its voltage will tell the alternator how much
juice to pump out.  So just charge ahead....

A fully charge battery will be 12.6-12.8 V.  When you first
stop charging, it will be up over 13, but quickly or slowly
drop down.  That's why you need to wait 24 hours before
measuring the "state of charge."  My UB12220s will hang
up at 13 for a long time, compared to my starting battery.
How new and strong a battery is makes a difference.

Here's a good link of info:
http://www.windsun.com/Batteries/Battery_FAQ.htm

Richard