Before we talk about the RCA's, remember that you also need to run an Amp Remote wire, and unless you do the loopback trick with the factory speaker wires, you also need to run some speaker wires to that amp. It might be a good idea to run a heavy-gauge ground wire as well just in case you need to troubleshoot ground loops later (although with just a single amp, that's unlikely to happen as long as you ground it well).

Now, on to the RCA's...

You will need to run two sets of RCA cables if you want your front/rear fader to work.

If you intend for the rear and front speakers to always be equally balanced and not adjustable (in other words, the front/rear fader does not work at all), then you only need the single pair of RCA cables.

How it's done:

Run only the empeg's front outputs to the trunk. In the trunk, you split or daisy-chain the two RCA outputs into the amp's four inputs, similarly to what's pictured here.

Then, you set the empeg's fader to center, and use the gain control settings on the amplifier itself to set the level of the front speakers and the rear speakers. It may take a few road trips before you're happy with the settings.