I have one emitting light garage safety switch on and the other receiving switch is off. How do I lign them both up in a 16' garage door? Is there a special tool to align same or what do I use to get the receiving light switch to activate. (It should turn green when properly aligned.

No special tools, Aim the transmitter to the receiver, then go to receiver and move around until you see a good solid green. Look down from above and head on to help alignment.
They are Nothing like aligning Long Range PhotoBeams, They are a little tricker, Should be easy for yours.