What I notice is that both Motion and FCP tends to fight for the video output and can end up with the application becoming very sluggish. If you need both to be running, when you switch from FCP to Motion, turn off the External Video to OFF and then switch to Motion.
I don’t think you need to do the same for Motion when you switch back to FCP coz by then you would’ve set to External Video to All Frames which then FCP will take over. But remember to switch is to OFF again when you go back to Motion.
CMD+F12 is your best friend when you do the switching.
-chrispy