I heat my water in the bottle and then drop in the formula, shake and feed. When the water is shaken it distributes heat evenly so don't have to worry about uneven heating/burns . I always keep a fast-reading thermometer on hand and double check each bottle before giving it to my LO.
The formula can says something to the affect of not heating in microwave to prevent serious burns. It doesn't say that microwaving will breakdown the formula or anything like that. Sometimes I will microwave mixed formula but I try not too.
I also think I am going to find a good thermos, like the ones that loggers use. It keeps liquid steamy hot all day. I'll just get the water to 100degrees and pour it in the thermos. BAM, instant hot water all day long. Plus, good for traveling! Now, where can I find a logger! LOL!
Good Luck.