... I recorded the amp on a setting I liked and adjusted the eq in Logic. Thats how I came up with the 500hz range. ...
Does Logic have a way for you to get a spectrum plot of your after-EQ track? [EDIT: apparently yes, though the video is old.]
Seems like a smart thing to do is look at your guitar track after the EQ and see how it has changed. Or since you know you apparently boosted at 500Hz, look back at Logic and see how many dB the boost was (it would be nice to know the width of the boost, but just for feel).
... I did run the calculator where I had the knobs set!
If the image in this post was how you had the knobs set, you had a pretty strong dip between 500-600Hz. And your Mid pot is down around 2-3. Turn up that Mid pot, and the dip will lessen. Might even sound like your Logic-EQ'd track.
In some ways, the typical tone stack is not intuitive. You might expect that setting each control at half is "flat frequency response". It's not.
And when you play amps with true "flat frequency response" the auditory impression isn't "flat response". Guitar is a midrange instrument, and most pickups make it even more mid-focused. This can be a very good thing in a Mix. But we're so accustomed to 60's amps (and their variations) which have a pronounced mid-dip in the tone stack that we come to think that mid-dip is "flat". It may be "balanced among highs, mids & lows" for the instrument by itself, and yet still not be "flat response".
In a track, every instrument will be heard if they contribute energy where other instruments don't. It's no accident the kick drum, snare & cymbals put energy in a different part of the audio spectrum. Your guitar will be more audible if you don't try to put a lot of energy in the 80-200Hz range where the bass may be competing for space. It's no accident that acoustic guitars in a band track often get EQ'd to occupy similar frequencies as the hi-hat (mixed to mainly hear the rhythm that player is strumming), to get out of the way of voice & other guitars. Might be a good idea with multiple guitar parts to have very-different sounding guitars, and/or very-different EQ for each (they might sound garbage when solo'd, but blend well together).
https://www.youtube.com/watch?v=aNwWzJLAwkI