Nice writeup and diagrams.
What I, and others, do is similar to one of yours.
Behind the panel, there is a single "common buss" for "+" and "-" that feeds all devices. Feeding that are 2 batteries, each with their own simple on/off master switch.
You then have 3 modes of operation:
-feed everything from battery 1
-feed everything from battery 2
-feed everything from both batteries at once. There is the previously stated issue regarding batteries at different states of charge, different ages, etc.

Plenty of our electronics can display battery voltage or add in a simple panel voltmeter to watch the "device side of the buss" to monitor battery/system voltage.
When voltage gets low, turn on the second battery and THEN turn off the first battery so everything remains powered.

I like to use screw type terminal strips to make it easier to add/remove devices.

These are nice since they've harder to short out.....
http://www.mouser.com/ProductDetail/...zIEaApPW8P8HAQ

These can be used with ring or fork terminals.....
http://www.mouser.com/ProductDetail/...NsEaAm_D8P8HAQ