MegaPI and raspberry power supply


I have the Ultimate 2.0 which I power through a powerbank that has a 12V barrel-connector and also a USB-connector. I only connected the 12V to the MegaPI. The attached raspberry gets its power through the GPIO-Pins which worked fine at first.
Unfortunately I seem to have killed 2 raspberry pi with this setup. I think that there was kind of over-voltage on the 5V and/or 3.3V-Pin so that the power management chip of the raspberry got damaged.
I would like to know whether you also think that this was the case and how I have to supply power correctly to the MegaPI and the raspberry so the nothing gets damaged.