That could be a problem. Android Auto takes over everything, unless there are settings or permissions you can alter to change it, I don't think you can run a phone through sync3 and a separate phone hardwired through android auto.
Just to justify the cost of Nav, I have tried to run the stock Nav with the phone plugged in, but I can't. It always goes to AA google maps and I haven't found a setting to change this. Seems like with the 401(A) package there is a lot of redundant ways to do the same thing. Sync3 doesn't work that well for me for controlling music through Bluetooth (not surprising). Android auto works well but has to be plugged in and takes over everything, essentially meaning I don't use sync3 anymore. If the car could be android auto compatible without the sync3 upgrade, that would have been the most practical approach.