ORIGINAL: PlaneHeli
I have 2 battery setups on all my aircraft. Often using different capacity batteries. Ive used this setup for a few years now.
As long as the voltage is the same there should be no issue.
I agree with PlaneHeli, I've been using a 1500mA and 2000mA going on 2 years now, no issues. Just make sure they are same chemistry and voltage.