An example of the type of adapter that you can use to put your software dongles inside your computer, out of harm’s way: Dual USB Header Port Adapter.
There are several of the same for USB3, but they are overkill for dongles.
I bought a 5 port USB pci card. 4 external and 1 internal. Works like a charm and no dongle hanging off the back.
My next goal is to build an internal port in my laptop for my other dongle.
My MB is for a workstation and so was designed with one internal normal (not header) USB(in addition to the normal headers.
However, I also have an iLok, so I have a little USB hub plugged into that socket.
But it just occurred to me that I have a couple of spare dual USB+Firwire back-panel brackets with internal plugs from old MBs, so all I have to do is remove the dual USB from a bracket and use that for the dongles instead. Better than the hub because at least I can bolt it down somewhere.
I have changed over to the dual USB back-panel bracket, bolted to the case floor. Works fine.