DNA studies can tell only which genes exist now, and that only in the sampled people. It doesn’t give geographic origins, or even much in the way of ancestry.
You are correct about what genes exist now and there is some discussion about the “first†Americans suffering a mass extinction of some kind. However, MDNA studies have proven very useful when tracing migration of the current gene pool. Along with bone analysis as correlation there is a strong pattern of migration developing. I suspect that we will find that there were three or even four distinct migrations in ancient times to the Americas.