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I have not had any experience with an EQ-6 but if it is going to be permanently mounted and you do a reasonable Drift Align I see no reason to do a PEC run, you are recording after the event.
Providing your PE is smooth and dosen't have sharp uncontrolled spikes, your autoguider will take care any PE. My previous mount, a G-11 and my current field mount, a GM-8, have PEC but I didn't/don't use it, my Observatory mount, a Tak NJP dosen't have PEC at all.
You can check your PE after you have set the mount up and done a DA by running PHD and using an autoguider and enabling the Graph under the Tools Menu, set it on 50 and watch the progress for a couple of worm rotations, you will clearly see any sharp spikes and you will see the autoguider responses.
Cheers
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