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I guess I was pretty lazy when it came to auto guiding setting. I had two lots of setting depending on what software package (SGP or MaxIM) and which laptop I was using. One laptop would change direction after a meridian flip and the other wouldn't, things like that. Setting were the same as far I could tell!
In PHD2 I used 0.5-1s exposures and just whatever PHD suggested I should.
In MaxIM DL I used a bunch of different settings. I actually found that sometimes 0.1s exposures, aggressiveness of 8, min move of 0 and max move of 0.3. The 0.3 was calculated from my uncorrected PE (I'd never attempted to correct for it), meant that even with the star jumping all over the place with sky conditions the mount couldn't jump too far in any single movement but would still be able to compensate for PE.
I found this worked best for my setup at 660mm with my EQ6 and guide scope BUT it was also the most unstable (guide camera dropouts) so I didn't use it unless I was babysitting it. If I wasn't, 1s exposures and MaxIM default settings (aggressiveness of 8, min move 0.01 and max of 2).
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