Both the Rough Polar Alignment and ProTrack are for SB mounts only I believe. The Rough Polar Alignment uses its homing sensors, something that the EQ6 doesn't have
What really threw me was that on my second iteration it didn't move far (was only ~3 arc min down and ~12 arc min East). When I went to move my mount East I found that TSX had moved in the opposite direction that I thought it should have. At first I thought I must have just read it wrong but when I did my third run I found that I was in fact ~24 arc min too far too the West (needed to go East), so it moved the correct distance but in the wrong direction from what I can tell!
Autoguiding is my next step to figure out, never done it before. Tried doing it in MaxIm DL a couple of times when connected to TSX but it never seems to be sending the "move" signal for calibration. I THINK I need to have it as "Telescope" and not connected directly to the ASCOM TheSkyX thing. More testing
Tried using TheSkyX to auto guide, just kept spitting out errors during calibration. I probably haven't filled out all of the information for it though, I don't think I have ever put my guider scope information and stuff in so that could be why.