Set Record Macro hotkey to overrule all other hotkeys?

I'm trying to use the Macro Recorder for recording a string of commands, however I want to stop recording using the same hotkey I used to trigger recording. Unfortunately at the point that I need to stop recording there is a window open from a previous action, so when I try to stop recording the hotkey command R applies to this open window, rather than Keyboard Maestro...
Which leads me to my question: how do I set the command R hotkey to apply to KM even when it isn't the front window? If there are any better ways to circumvent this issue then I'm all ears!