I need to program four motors to the joysticks. Two motors will be tied together with anaxle on each side of the robot and be run by a joystick. Those motors are reflecting, so i will need to add the bMotorReflected statement for one motor on each side. But then the 2 groups of the tied motors will be reflecting each other as well. If i reflect 2 motors that are diagonal to each other, will they all run the same way?

It's hard to tell without seeing your setup. The best thing to do is write your code. Then only plug in one motor at a time and verify each one is going the correct direction.