How are you applying the second and subsequent layers of epoxy? You may want to try another technique. As in if you are squeegeeing, try rollering. I personally didn't have much trouble with runs, but I also worked smallish areas rapidly and thinly. Are you working large and thick? Also, how slow settin an epoxy are you using. I'll be the first to say I like a slow set for working time, but if it's taking 2-1/2 days to become tacky, it's going to run.

A usefull tool for me in dealing with runs after they harden is a hand plane. In a second, maybe two, it'll skim off a run.