Do they lower sound quality?

Supposedly, they work by converting the signal into optical, breaking the electrical connection. Dunno exactly how they pull it off, but as Hugo said, they don't necessarily have the full range of frequencies and you might lose some of the extremely low frequencies. Like Hugo said, I wouldn't worry too much about it if you don't have a subwoofer. Most regular car speakers can't reproduce those low frequencies so you won't miss them.

Someone once posted a description of the frequency response of a certain brand of opto-isolator, and it sounded pretty good. The one by Radio Shack, however, doesn't pass the low frequencies well. Anyone have a link to the good one so that I can put it in the FAQ?

they put them on backwards according to the markings. What's the the difference?

They are just two independent line-level channels. So if they made them backwards like this:

Empeg Left ---> Isolator Right In--->Isolator Right Out---> Amp Left
Empeg Right ---> Isolator Left In--->Isolator Left Out---> Amp Right

Then it makes no difference at all.

How to check: Move the balance and fader controls on the empeg and listen to make sure they go in the correct directions for all four channels.

Finally, understand that ground loops can (with some care and time) be solved without using the isolators. An isolator is just an easy/quick fix. Please click here.