You need to deal with it on all fronts: low carb diet (ketogenic is ultra low carb), antifungals (both oral and Nystatin enemas), supplemental HCl capsules, and laxatives if you need it (I recommend Miralax or generic equivalent.)
I always considered seeing candida in or on your stool as a bad thing (it's thriving in your colon). I know people who think that if you see it in your stool it must be dead. I'm pretty sure that dead yeast gets incorporated into the stool and you don't see it.