Question I heard that you can't run ez app trains at the same time? True?
That is incorrect. DCC and EZ App locos can run on the same track at the same time. You just cannot control an EZ App loco with a DCC controller and vice versa.
How do I select which one is in control?
Both are in control at the same time. DCC locos will respond to DCC commands through your DCC throttle and EZ App locos will respond to the smart device they are connected to. They two systems are completely different. With EZ App the loco is only getting power from the rails. It doesn't matter if that power is from DC or DCC. It isn't reading the DCC signals, just receiving power. It will do nothing until a smart device tells it to do something.
I tried to follow instructions to get the app to accept my engine. After repeated tries with bluetooth on still no results on DC and DCC track.
More info is needed. What type of smart device are you using? Does it have Bluetooth 4?