Where do the return currents go for a MCU with multiple Vdd and grounds?
Doesn't matter.

Every Vdd will have a decoupling cap. 

So as your return current follows your signal, it will internally go to whichever power pin has the least impedance, and then go to ground through again, the path of least impedance, which is most likely through the decoupling caps.

So knowing which power pin, doesn't matter. Have decoupling caps, and a ground plane, and the currents will do the rest.