There’s no “set” way to do this, but there are small white nylon spacers that come in the (small?) hardware bag that I think are meant to serve as standoffs and you screw the mega into the back of the frame. Probably could also hot glue or ziptie it in place. I’ve seen someone cut a small mount on their machine. Personally, I opted to 3D print an enclosure for the electronics, which also mounts a 80mm computer fan to it. That way, I had some cooling for the motor controllers.
There is an option in Ground Control which enables the Z-axis. When this is disabled, it will prompt you every time the program changes Z heights and you can go to your router and set the depth yourself.
I did the same when I set mine up, just wanted to save some time. White it is not necessary to get cutting, the kit really helps with accuracy. I have a couple of deep groves cut in my spoilboard from cutting my “final” sled from me setting the final depth too far through the part.