At first I had trouble getting the shakes down, too, for me it was the texture. Not that they taste good, I use nystatin in mine, so they taste HORRID!
However, I found that adding very cold water to them helped- warm makes it worse.
Then.. I *don't think, just drink.* Down it goes, wash the blender, and that's that.
Once or twice a day is fine for the shakes. Sometimes I feel that my body needs a break, and then I take a few days off. In the meantime, I usually up probiotics and nutrients for healing.
Another helpful practice has been enemas. Seems even with the shakes, it is hard to get the candida loose and out.