Can I make Xephyr toggle user keyboard and mouse?

I need to pilot an X application with my PC, to take scientific measuring. I have an xdotool script which does the job pretty well, but while it's running, I cannot use my PC, which is frustrating and cumbersome. So I thought I can run the application in a separate X server, while working in the principal. I managed to start the application and make it work in **Xephyr**, but it's fragile: Xephyr acquires my mouse when its window is visible, and it's not necessary to be focused. The grabbing function (Ctrl+Shift) kinda works, but only in one sense: I can grab the mouse, but I cannot make it **ignore** it. So my question is: is there a way to make Xephyr selectively ignore (it should be toggled on and off) my mouse and keyboard, much like it happens with a VM on VirtualBox? Thanks!