New Blog Templates: What is my main site?

Hi my New Blog Templates is telling me the second site I made is my main site. Maybe I'm confused on the terms.
My url, in the root on the server, is mydomain.com. In this root I'm making my main site...or so I thought, to advertise it, put the sales pages, etc.
Then I made mydomain.com/site1.

New Blog Templates is telling me 'site1', which I chose to be my template is my 'main site' and I cannot template that. Is this correct? The 'site1' is the one I want to use as a template. Thanks.