my gain is all the way down

Unusual, yes, but not impossible.  The function of a gain is to match the receiving unit's input to that of the sender equipment's output.  Like, for example, an amplifier receives a signal sent from a head unit...so the amp's gain is adjusted to correspond to the head unit's output.  By matching the units, the object is to maximize signal strength while keeping the signal / noise ratio as low as possible.  You want to be able to turn any gain enough, back and forth, to find the right spot.

And, an amplifier's output is what it is...whether gain is set to minimal excursion or to full max.  It may not output, at any given time,  even close to the published specs but it does have an output (that is dependent on other things than its make and model.  Those things include the vehicle's power supply, wiring and grounding).  Therefore, I couldn't tell you how many watts it can achieve on a beautiful day.  But the gain doesn't add to output or take away from it.

So yes, you can have a setup where any given piece of gear isn't perfectly compatible with the next piece of gear up the chain.  When you have a case where a gain is set to minimum and the gain setting tests can't be properly performed (as in gain at minimum with no play for adjustment), you have a mismatch of gear.  In most setups, this likely isn't a problem at all.  The sound may be quite good even though the adjustment can't be as finely tuned as you would like.  You always want to be able to adjust from a known bad (clipping) to a known good (clean).

You  have to take extra care in your setup because you have another intermediate unit thrown in the mix, the EQ.  And you will especially run into some headscratchers because you are working with a less-than-ideal quality music source in the ipod.

It doesn't matter where you set the sub control.  You are not adjusting power output but only positioning the volume of the sub to a relationship to the volume of the rest of the music.  And you can't take for granted what any unit's voltage output should be according to where you have positioned a knob.  Adjust gains from original source on down the chain using established methods.  Search 'gain' in the google box on this site's opening page and also read the sticky in the audio hot topics forum.

If you learn anything after a successful audio setup, it's that you will never again refer to gain position as "halfway" or "one third up" or anything that refers to relative position of the control.