Is it ign. noise or alt. whine?Ign. noise is more "staticky" sounding a buzzing/ticking sound and increases in speed with RPM.
Alt. whine is a whistling kind of sound and changes pitch with RPM, kind of like a siren, it gets louder as you load down the alt., turn things on, [head lights, rear window defog, step on brakes and so on].
There are a number of ways "noise' gets into the audio system, poor grounding, or ground loops is one of them.
It is unlikely that any speaker leads are connected to the EQ, the EQ will be connected to the HU and the amp with RCA interconnect, from the HU to the EQ with one set, [pair] of RCAs and depending on amp from the EQ to the amp with one or two sets of RCAs.
To check where and how the noise is getting into the system I would start by bypassing the EQ, unplug the RCAs that run from the EQ to the amp, see if you still have noise, if not, plug the RCAs directly into the back of the HU, and check for noise, if you still have noise, the EQ us not the problem, on the other hand if you do not have noise, then the EQ is the problem.
Let me know what you find. 
94
94LS
^^^ now in the process of being striped down and gutted for the rebuild.
Now cruising in my new winter car, 89 Chrysler Dynasty 
You get what you pay for.
Nothing is impossible, the impossible takes longer and costs more money.
