Engine noise can be frustrating. Luckily fixing it is simple.
Put ALL grounds from ALL devices, EQ, Head Unit, Amp, Cigarette lighter if your playing from a phone or iPod that's charging, everything all to the same point. A distro block right off the battery is preferred.
The whole reason you have engine noise is because the grounds have an impedance mismatch and have to travel through other parts of the system to find a common point.
If you have done all this and it does not work, ground your head unit to your eq, ground your eq to your amps, etc. basically making a ground wire tethering all of them directly to one another's chassis.
Basically all devices in the system need to be at the same ground potential.