I see it's been a week since you posted this so I'll jump in. I do NOT have a Sub anything; used to have a Little Phatty (which had the same side panel) but now only have a Minitaur, Taurus III, a few Foogers and a vintage Minimoog so your mileage may vary but most of what I'm about to say will apply.
You can plug in/unplug expression pedals without any concern. Moog takes lengths to make their products tolerance to the small spikes in voltage that may be present and the holds true for the Mini/Moogerfoogers and synths.
You can change patches with the pedal set to different points; no problem here either.
Yes, the sound that you hear will be different with he pedal plugged in depending on the position.
The full TOE position should be unattenuated assuming the EP3's pot/knob is set to be fully open and therefore the sound with pedal in or not should NOT make any difference; (you should test this and confirm; maybe post here so that others will be helped).
Full HEEL position will fully attenuate the voltage which, if my memory serves means that in the case of the Filter, you will hear near nothing, as if the Filter Cutoff was fully CCW (counter clock wise). If plugged into Volume CV in, it will result in no audio coming out of your Sub.
In no case will the full TOE position be any higher than the setting on the panel or within a given patch meaning that if your volume is set to 5 on the panel (out of 10), then a full TOE position can only be as loud as 5. Likewise for Filter.
I really don't have a guess as to how pitch is affected. I believe this is best controlled with an external LFO or a pitch controller in which case it may be taken as relative (in the former case) with center position of the pedal affecting 0 change and up or down a voltage positive or negative... OR may be absolute with the base voltage of the keyboard (e.g. press any key) representing the HEEL and a max of 5v representing TOE on the pedal or a full CCW on a sequencer step that may be coming from a Deeper Dark time or at the top end of a ribbon controller. I believe that this is the way that Pitch is dealt with.
Finally, the knob on the right side of the pedal further attenuates the output of the foot pedal such that if open all the way (turned fwd all the way) that the output of the pedal is 0..5v (if 5V is the ring voltage); if turned back 1/2 way, then the full range of the pedal is 0..2.5V, etc.
Keep in mind that the EP-3 does not SUPPLY any voltage, rather it attenuates (will reduce) voltage; meaning that any voltage applied to the ring connector (of the TRS plug) is attenuated and returned on the Tip of the plug. If you have a synth that has a 10V signal across the ring, the output will be up to 10V but as this is just Moog pedal in a Moog synth, the 0..5V applies.
Hopefully this helps somewhat. Otherwise, check this link for the 'manual' such that it is:http://www.americanmusical.com/itemfile ... manual.pdf
This is for the EP2, the diff being:
EP-3 uses a cog, not a string for action (EP-3 is better/should last longer)
EP-3 has a removable cable so you can use a longer cable if you like
EP-3 has a polarity switch on the bottom
Good luck, hope this helped!