It is sounding like the Amp is duff as with no inputs to the Amp, the Amp outputs (RG&B) should also be off.
Have you checked that both reels work correctly when connected (in turn) to the controller output with no Amp connected?
Connect the LED controller and the Amp to just one power supply (as it looks like you are using 2 seperate supplies), connect the Amp i/p's & o/p's as you did before then do the following:
Select red on the remote control - what colour is 1st reel/2nd reel?
Select green on the remote control - what colour is 1st reel/2nd reel?
Select blue on the remote control - what colour is 1st reel/2nd reel?
Select white on the remote control - what colour is 1st reel/2nd reel?
Select off on the remote control - what colour is 1st reel/2nd reel?