Right thrust *does* work the wrong way when you're inverted and with most profiles you're faced with either just learning to apply the appropriate amount of (usually) left rudder when inverted or ditch the right-thrust and learn to apply left/right as appropriate.

Since a really good 3D flight will see the model flying inverted for about half the flight I'm starting to switch to zero side-thrust and just using the rudder all the time. It becomes second-nature after a while.