ive used Schottky Diodes before for dual inputs before but im wondering if the "switch" is immediate? Trying to provide power to a gps module until it gets a gps lock then power up rest of system without the gps module "rebooting"...

here's the circuit:

 

That looks like a good solution.

There will be a brief period of overlap of conduction as the input to one anode drops below that of the other, but that is a good thing. There should be no dropout of power to the GPS module. I have used that method several times, getting into a complicated switch-over circuit is not worth it to save a few hundred millivolts, at least in my applications.

You may want to raise the flight controller's 5V supply or lower the battery backup voltage by a hundred millivolts or two and keep the diodes in thermal contact with one-another to assure that no significant current is drawn from the battery. Alternatively use a Schottky for the flight controller 5V connection and silicon junction diode for the backup supply.