Here's what happens.

The two voltage regulators will have slightly different voltages, they always do. Let's say one is 6.00v and the other is 6.02v.

When the plane is sitting there with everything idle all the current will be coming from the one with 6.02, that's the way they work. The other one won't start to let current through until it's output goes below its set value of 6.00. This means that the one with the lower voltage is actually both a backup and a "fill-in".

In high current draw situations (which happen more often that you might think) the lower voltage regulator kicks in and adds its supply to the other one. If the higher voltage one fails altogether the lower one then flies the plane alone.

So either have both batteries the same capacity or have the bigger one on the regulator with the higher voltage. But don't try to mix Nimh and Li chemistries.

And on the next flight turn on one battery pack at a time and test each pack alone before you fly. It is possible with this setup, if something went wrong on the previous flight, that you could have landed on one pack without knowing.

TF