One way of paralleling batteries is by using Schottky diodes and say a jumpers during battery change over

 

@ericgibbs Yup, that's one way, however my prototype aims to be as light and slim as possible. Unless mistaken, this idea would require 2 seperate battery compartments.

 

Why do you think you would need two main battery compartments.??

Two AA batteries in a portable holder and series diode, with a short lead that plugs in parallel with the existing power wiring, while the main battery is changed, then unplug the portable 3V battery pack

 

@ericgibbs Would you believe me if I told you I already implemented a similar setup? Except I'm using a 9V battery from an RC Car. This circuit works no problem!

Still, if I can figure out a better solution (which would remove the need for an external battery) that would be nice!. I've order 2x 10F caps and will try them on the input side, before the boost converter.