An example of an ascending sextuplet (groups of 6 notes) run I'd do is: three fingers per string pattern of, say, Amin starting from 6th string 3rd fret (g), but when you reach 5th string 5th fret (d), go back to 6th string 7th fret (b). That is a six note pattern (5 steps up, one double step down), which, when applied to other string pairs, produces a run. I guess it's Paul Gilbert inspired, though it's not neccessarily alternate picked.
Use runs a lot while practicing and they will fall into place. Start from any of the current_chord tones, go crazy, and try landing on one of the new_current_chord tones, even if it isn't the highest you can reach with the run.