The empegs fader, yes, though the headunit, which drives the
speakers (or amps?) probably has its own fader control.
Equalizer - yes you'll lose the ability to separately affect
fronts and rears. But you can lock it in 2 channel mode and
get 10 bands per channel instead of 5 - though 5 parametric bands probably are enough for most any user...
I can't think of anything else you'll lose by going through
a head unit - any one else? You do gain the ability to have
sound in the car even without the empeg.
_________________________
/Michael