BMI and ASCAP are what are known as PROs ( Performing Rights Organizations ). They serve many purposes but you can kinda think of them as a guild or union of sorts. They not only collect your publishing royalties ( I believe that they keep 50% though, so thats sometimes tough to chew. ), but they also go to bat for you in the case that someone infringes on your copyright. In addition to this they usually provide many resources and workshops that can be useful to many different types of people in this industry.
It is my understanding that many people just wind up going with whichever. They either know a rep, or have met someone through networking, or visited the website, or all of their favorite artists use that one, or whatever. I am sure that you could study more and find a more logical way to do it, but that is up to you. They are both very good at what they do, I am sure.
Are you APPEARING in a commercial, or is your music being played in the commercial?