On the Mac Pro, the easiest way is to intercept the wires going to one of the front USB ports and tie onto them. Depending on which Mac Pro, there are different ways to do it, but it's really just a header/connector on the logic board. I'm not sure on the '09/10 models, but on the '08 model I think it was two standard flat connectors just like most any PC uses.
On a typical PC, this is super simple as most PC motherboards usually have a USB header on the motherboard for attaching to the front or top of the system case.
I keep my USB dongles all connected to their own USB hub. If I need to keep them secure, like on a DIT cart, I would put that hub inside a lockable cabinet - secured into place and run a USB cable to it through a small hole. I actually don't have any dongled apps that I take on my DIT cart anyway...
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