I have been having a look at this issue too for a 5V Pro Micro based portable device that I want to power either with batteries (using a 5V step-up DC/DC converter) or USB. The best I could come up with, though I have not made it, is an op-amp based power source selector. Example:
http://www.edn.com/design/analog/436830 ... r-selector
I do not understand the electronics yet but you use op-amps as comparators and the mosfets switch between the input lines.
I think the full-sized arduino schematics have a section in them that allows you to connect and disconnect the USB power while batteries are connected. If you look there you may get a power source selection circuit. Some people have critisised it but it obviously works.
I also had a look at "power path management" because Li-ion powered circuits also have to deal with selecting power from charger or battery but I did not really get anywhere there due to patience/understanding issues. There seem to be dedicated chips for that.
Maybe another solution could involve a 2 position mechanical switch that allows either battery power OR usb power to be on. This way you can cut off one and supply only the other. If it is a 2-pole-2-throw (2P2T) switch you can also switch grounds.
Advantages: simple, cheap, can be done in minutes
Disadvantages: not so elegant, have to hack open a USB cable
Then regarding your high-current devices, power those independently of how you power the Pro Micro.
First post! Woot!