To do this you'll have to trigger the command on one, and use a condition to check for the other.
E.G.
If you have the "When I press button" option set to button 3, add this to the top of your command:
Begin Device State Check : Keyboard Key 'Ctrl' Is Pressed
End Condition - Exit when condition not met
This means the command will be executed(you'll see it in the log), but not actually do anything beyond checking for Ctrl, before exiting.
If you want to also have a command execute when Ctrl is not pressed, you can have have the actions for both possibilities in the same command and use the condition to execute either branch, or invert the condition and have two separate commands(one key/button press can trigger many commands).
If it bothers you that the command appears in the log each time you press the button, you can use the "Ignore an Unrecognized Word or Phrase" action to hide it(despite the name and description in the action list, all it does is hide the command execution from the log).