domain management

new to the wordpress scene…

…looking to create a topic-specific blog combined with topic-specific directory

what is best way to manage the domains so that

“site.com” is separate from “site.com/blog” and separate from “site.com/directory/category1/*.*”?

there may be some other sub topics that would need their own sub-domains, so looking for some guidance on how to go about this in WP?

ultimately, feels like the “site.com” domain will be a programmed index page linking to the blog, directory, etc. — just want to get this set up correctly up front so don’t have to go thru pain down the road redoing domain site map

thanks…