Domain with email mapped to multi-site subdirectory??

I have a reseller hosting account, so I can set up as many domains as I want with email, etc.

If I set up a new blog in multi-site with a domain mapped to a sub-directory, it would seem that the domain is no longer available for email addresses. Is that correct?

Or is there a way to keep the domain active for email addresses while at the same time having it mapped to a blog.

You can tell I’m confused .. sorry about that..

I’m sure the answer is simple ..