Here is how you take command of the AT-AT.
Take an infiltrator unit and have him ENTER the AT-AT (or AT-ST, TMRB, or any vehicle that can carry troops) by SHIFT + Right Clicking on them. Not there is not a 100% chance of this working, so send more than one infiltrator to do the job. Or freeze the armored unit with a zap from the Y-Wing ion cannon- then it works every time!
There you go!!!