Hy has it correct. You will have PHD2 running in a separate window, but the calls to begin guiding come from Ekos along with the dither settings (the PHD2 devs recently made it clear that dither settings is job of the imaging program, PHD2's job is to make the telescope move in the way commanded by the other program). Everything else you would do from the PHD2 UI you still do there - run Guide Assistant, set min-move and aggressiveness values, set camera binning and exposure time, etc.

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