Apple - Natural Scroll Direction: On with trackpad, Off with mouse
Hi just found a great app that totally fixed this and so simple! You can set the scroll direction for each device separately.
SCROLL REVERSER http://pilotmoon.com/scrollreverser/
Try this:
Go to Accessibility settings for Mouse & Trackpad in System Preferences.
Tick the
"Ignore built-in trackpad when mouse or wireless trackpad is present"
option.
Then, with your mouse connected, go back to your Mouse settings in the System Preferences and adjust scrolling accordingly.