when I plug mine in, I am asked if I want to use it to control everything. I just say no. Should also be settings in both TV and VCR to toggle if not prompted. You can always change it later if you feel something is wrong. Perhaps I'm mistaken, but I don't seem to be having any issues.
Also, if using the apps on the TV, you should connect a separate audio cord for tv-to-avr audio. I just use the toslink on my sony as there is no coax option.