I am not sure what you mean by the throws aren't equal. Are you saying the travel up is more or less than the travel down? or that with the stick in neutral one aileron is higher than the other? Or one side travels up and down more than the other?
On a computer radio check the throws electronically to make sure that you have equal travel. Make sure trim is neutral.
If all is well and the travel you have is within limits go fly.
However if one side is higher than the other adjust mechanically with the clvises or the servo arm.
good luck