I also run my empeg (rio-car) as the only head unit in my car, I use an xtant amplifier with built-in crossovers.. it's highly doubtfull that you have the wrong amplifiers, since the empeg is designed to work with almost all car amplifiers.

the problem is the crossover settings for your front speakers, as other people have said.. the EQ is not designed
to be used as a crossover, and is not designed to work in the way you are using it.

you simply need to adjust the crossover settings on your front amplifier, and rear amplifier to get the desiered output. a local best-buy car tech should know enough to be able to adjust this.