I just redid my panel and have used individual three-way on-off-on toggle switches together with a DIY MOSFET circuit to enable switching each instrument between battery A or B in flight.

The circuit itself needs a few components (2 N-channel MOSFETs, 2 capacitors and 4 resistors per channel) to facilitate switching in-flight without dropout, but they're all surface mount and the overall circuit isn't much bigger than the simple bus bar it replaced:

http://i.imgur.com/gGsPTU2.jpg

The benefit over running everything off a single battery at a time is that each battery should hold up better with the lower current required from each individual battery, but on a long flight I could separate "priority" and "nice to have" instruments onto separate batteries if power gets low, and I don't need to decide what the configuration might be in advance.

The capacitors on the MOSFET gates give about 2-3 seconds switching time when toggling from battery A to B or vice versa through the "off" position, ensuring flight loggers etc continue to work.

I've also added a simple "always on" channel with a couple of diodes for the gear up warning.