I have an EQ in my amp's effects loop and am struggling to figure out the best way to set it up. I've tried flat settings on the amp and then changing the EQ in the loop. Tried setting the amp EQ by itself with no effects turned on and just the guitar plugged in. Tried the method where you play chords on different strings until you hear a sweep in the frequency when turning the pots up and down, etc. It seems like when I find something that sounds really good it that it doesn't sound right when a different effect is on or if I'm standing in a different place or something.

I know it's not an exact science, but I was wondering what other people are doing to make their EQs work with their amp's EQ. The biggest problem is I seem to never be able to get the mid's dialed in where I want them.
I usually just use my EQ to get a tone other than the tone I'm getting from my amp already. So I dial in a good EQ on my amp, and then I use the EQ for leads, mid boost, or for extra punch when needed.
If you want to use the pedal as your main eq all the time, I say dial in a satisfying tone from your amp alone. Then put in the pedal and try adjusting each individual slider until you find a tone you like.
Fender Highway One HSS Strat
Art & Lutherie Cedar Acoustic
Line6 UX2
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Basically find the best tone you can from the amp, then fine tune it with the pedal.
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Usually I do like stated above... Get a nice tone via the amp eq then tweak from there. But currently with my rig im doing the set everything to 5 and dial in the tone via the eq pedal. Either way works its just prefrence and if you like what you hear. Also it depends on just how much adjustment your onboard eq has in the first place. If it has minimum range you might want to just set them to 5 and go full eq. But if you can get a decent range out of the onboard set it first them tweak from there.
The amp is a hybrid 2 channel amp. Channel 1 is a clean/overdrive channel with volume, crunch, bass, treble controls and a tube preamp. I use channel 1 only for a crunchy overdriven tone and it works good for that. Channel 2 is a solid state clean/distortion channel with volume, gain, bass, mid, and treble controls. I use channel 2 only for cleans and will kick on a distortion pedal if I want distortion. So the onboard EQ is pretty lightweight but I otherwise like the amp a lot.

The EQ pedal is plugged in the effects loop and has lots more control and frequencies than the amp's onboard EQ. I'm going to experiment with it in front of the amp this weekend.