Connecting GNDs of a 50v, 30A and 9v, 1A circuit?

[HacknMod]

I'm building a self balancing unicycle which uses 9v and less than an amp for it's "brain" circuitry. However, I also have a 50v supply which is supplying power to a brushless motor at about 30A. The grounds of the two power supplies need to be connected (of course), but I'm worried about noise from the motor affecting the 5v circuitry. I currently have it configured such that the boards are connected through a simple molex connector as shown in the diagram below.

What is the best way to connect the grounds to minimize voltage spikes, disturbances, over-current, etc?

Thanks!