Does it matter?

I would like to fine tune the EQ after the procedure.

AutoEQ tunes your flat setting to "flat hearing".

Before AutoEQ:  Flat PRE > Flat EQ > Amp > Speakers = Not-Flat Sound

After Auto EQ:  Flat PRE > Flat EQ (AutoEQ ON) > Amp > Speakers = Flat Sound

...................or:  Flat PRE > Adjusted EQ (AutoEQ ON) > Amp > Speakers = Not-Flat Sound, but EQ'd to your taste.

At least that's how it works in theory.

So, Auto EQ creates its own settings that are not based on what the EQ was manually set to before the procedure?

Or, do I need to set the EQ to my taste before the Auto EQ is performed?

User EQ is set to flat automatically during the AutoEQ calibration process.  You have to EQ to your taste afterwards if you do not like AutoEQ flat (when ON).