I don't have an iOptron mount, but rather a Sky-Watcher (EQ6-R Pro), that I use with the mount's built-in PEC. I trained it on Windows using PEMPro. I think I saw somewhere that some models of iOptron mounts don't allow guiding and PEC at the same time (which is incredibly stupid if that is the case). But if that isn't the case with your mount, then there would be no other reason why you couldn't use it with Ekos and PHD2.

BTW, the new internal guider in Ekos has the same Predictive PEC ability that PHD2 has, so that's one more reason to use Ekos guiding instead of PHD2. And yes, you can use PHD2's (and Ekos) predictive PEC in addition to the mount's built-in PEC. They complement each other. They even say so on the PHD2 website in the documentation for the Predictive PEC algorithm.

Read More...