The probiotic works better on an empty stomach. We give it to him with a little juice mixed with water. I know a little legal sugar can help get the bacteria to start eating and doing their job!!!
I always try to take my probiotics before I start to eat a meal, as I have read that the stomach acid is lowest at that time. If I forget to do that, then I take them btw meals. If I really need them, I take them whenever as I figure some of them will make it to my gut no matter what.