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I used to go that way (Fiddling with PHD2 on the fly) but using Voyager has enforced me sorting it out then leaving it alone for Voyager to drive the whole show. Voyager is very much an integrator, it is the only program I manually open (I don't even do that really, my imaging rig is configures to start Voyager on boot) Voyager opens and controls everything else, EQMOD, PHD2, plate solving and planetarium (Though I rarely use that)
Once set up I have found it better data acquisition wise to just set it going and leave it alone.
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