I am not a grad student, but I have been a postdoc at CU Boulder (or rather JILA) last year and seen the crowds of students being led around on recruitment day and talked to the faculty around about how the numbers developed.
First off, JILA is top notch in AMO, so jumping across from biomed engineering will not be the easiest task and will require a lot of hard work. I suppose you have already done all the necessary coursework to be admitted and have reasonably good grades. The typical way to go to a PhD is to start straight after the bachelor, but this is not necessarily the only way.
The recruitment day last year saw a reasonable number of students, but a good part of the people went elsewhere. Part of the reason may be that Boulder is a nice, relaxed and sunny place to live, but for a pretty moderately sized town, living there is pretty expensive. That turns some people away. The real AMO groups (Jun Ye, Debbie Jin, Eric Cornell, Cindy Regal and maybe Heather Lewandowski) are pretty small and do not have too many people. Those who make it there are really good. So even if you make it, there is still a reasonable chance that you may end up doing a different topic. There are other groups working on topics ranging from biophysics to chemical physics and quantum information.
If you have some doubts whether your background is sufficient contact the people at CU. They can usually provide you with a good estimate of your odds.