"the origin is at the top-left of the screen and the Y-Coordinate increases going down, while the X-Coordinate increases to the right like normal. I guess my question becomes, do I have to convert the screen coordinates to Cartesian coordinates before applying the above formula?"
If you were calculating the angle using Cartesian coordinates, and both points were in quadrant 1 (where x>0 and y>0), the situation would be identical to screen pixel coordinates (except for the upside-down-Y thing. If you negate Y to get it right-side up, it becomes quadrant 4...). Converting screen pixel coordinates to Cartesian doesnt really change the angle.