Well, in your hypothetical example, you will be applying to CU's physics department in either case; you may (and probably should) specify an interest in AMO if that's what you hope to do there, or you may say that you're undecided as to what research you want to pursue, but it's the same application process either way. I would say this is likely to be the case for most fields/schools.
Many applicants don't really know what they want to study, and many think they know what they want to study but will change their minds as they learn more about other fields; the admissions committees are aware of this, and once you're in no one will care too much what you said you were interested in on your application. (Most people don't start doing research in their first year, and it's up to the individual professor who they accept into their group.) That said, it's a good idea to tell them what you want to do anyway; it helps the admission committee get a rough idea of whether everyone they admit will realistically be able to find an advisor in the field they want (and whether all the professors looking for new students have some potential recruits
Your lack of research experience in AMO (or whatever) probably won't be an issue as long as you can discuss the reasons why you're interested in that particular field, and (hopefully) how your prior research experiences have informed this decision.