I previously had a simple remote that allowed me to turn the LED strips on my motorcycle on and off when parked, which then I also wired in a separate relay so that the strips turn on with the ignition switch. The remote was switched on the positive line, so it made things easy. Never had an issue, it worked like a dream for the past 4 years.
I now have a 2 channel LED remote that has a function that alternates a strobe effect on the two channels. The remote is switched on the ground lines, not the 12v+. when I connect it up, and try the alternating flash setting, it doesn't alternate between the 2 channels, they both strobe at the same time.
I am trying to isolate the 2 channels using rectifying diodes, but I don't seem to have it right. I did up this diagram to show what I have now, thinking that the diodes would have worked in that configuration, but no joy. should the diodes be going on the 12v+ side?? Help me out please. 
Best Answer
Your diodes appear to be connected backwards. Current flows from Anode to Cathode in the direction of the arrow, which needs to be towards Ground. I have modified your diagram with the correct diode polarities, and showing the complete circuit with what (I think) is inside the black boxes.
Two diodes between the LED strips and the ignition relay contact would probably be enough to isolate the LED strips, but the extra ones won't hurt.