Using X-mouse with Retroarch

How do I use “X-mouse Button Control” on retroarch? X-mouse button control is a program that allows you to assign keyboard commands to buttons on your mouse, limiting keyboard traffic while you play. If your using a mouse with more than two buttons and a wheel you can free up a lot of your keyboard.

I think Retroarch is blocking signals from outside programs like X-mouse, is there a way to stop this?