Either way. Sometimes starting out, especially if you are sensitive to fermented foods, it may be easier to consume with a meal. Some people think that if you consume on an empty stomach it has a better chance of populating the intestines. I would recommend just doing whatever feels right to you though.
I agree with AlexP. In fact my favorite way to enjoy kefir is to use it in place of milk on my morning bowl of grape nut cereal and fruit! On the days when I switch breakfast to a hot meal, I just drink it throughout the day.