Anybody got any experience in mapping a domain to an MVC area?

Here's our situation:

Old system (still active but will soon redirect to new store):

www.example.com - our main site where we send traffic
store.example.com - our store site which is a completely separate site that is indexed in google

New system:

www.example.com - same site as before
www.example.com/store - new store site - built in an ASP.NET MVC area

Because store is a separate domain google gives it a separate entry in the search results. I'd like to keep this benefit in future but wondering whether or not there is a good way to map a domain (store.example.com) to the MVC area or if its just going to be more trouble than its worth.

PS. I'm not trying to keep existing indexing - its a completely separate store so thats not possible. I just want to redirect to the corresponding page in the new store. I'm just trying not to lose the benefit of two domains for SEO purposes.