Here is the website that explains some of the differences: http://www.gardenoflife.com/detail_primal_defense_ultra.shtml
It appears the only real substantial difference is that the ultra contains Saccharomyces boulardii which is a probiotic yeast and a pilot trial study (not a controlled group) suggests that taking it help people with UC go into remission. I am taking this particular species separately, but it might be nice to have an all in one. The funny thing is that the normal Primal Defense (something I've tried) mentioned this probiotic but only contains the enzyme, which I am not exactly sure what that entails. Also, one mentions the number of bacteria (5billion/capsule), but the other doesn't, only the mgs, so I don't know how they compare exactly. With any probiotic it shouldn't matter if you take more a day (however, there is strength in numbers), only it is typically a good idea to start any gradually, because having too much can cause an initial reaction.