Do not merge the outputs. Use only the front outputs from the empeg into the aux-in of the CD player. The front and rear outputs of the empeg will sound identical when the fader is centered, you don't need to merge anything. Just use the front outputs.

It's unlikely to be caused by the 4v outputs. FAQ entry on 4v outputs is here.

Read through the rest of the FAQ entries in that section about ground loops. Also keep in mind that when you use the CD player's aux-in, you are supposed to have the empeg turned up relatively high (maybe even all the way up to 0db) and then use the CD player's volume to control the overall output.

If you have the empeg turned down really low, but the CD player volume cranked, that might be why you're hearing noise in the system.