Too bad I didn't know... I could have sold you my Tuffy stereo console since I don't use it anymore. :-) I bought it when I bought my empeg so I could mount a cdplayer in there since I didn't think I would enjoy not having a cd player. I was wrong about that one! Never used the cd player again.
Anyway, I did it exactly opposite of you. I installed the empeg in the main stereo slot hooked up to the factory wiring, then hooked the output of the tuner/cd player in as "Aux" input to the empeg. I used the factory wiring for my speakers and ran them to the two amps I have under my rear seat. I also just spliced the power from the tuffy head unit into the factory wiring for the Jeep and it worked fine. I believe I also got a higher rated fuse as well since I was powering two units instead of just one.
A problem you might run into is heating. The empeg runs warm, and has vents on the top to facilitate airflow. Since the Tuffy is vertical and doesn't have much room on either side to 'breathe' (and it is steel with no ventilation) you might want to drill some holes in the proper side to let some air in.
Just some things to think about.
empeg + Jeep = rox!