Your main site can can have links to any external URL -- for example, https: // example . com or https:// your . subdomain . com.
Does that answer your question?
Yes. You can make multiple local sites, each pointing to sub-folders of your main local site. Simply ignore Dreamweaver's warning that your site folder resides inside a folder of another local site. Then, when you set up your remote connection, point to the relevant sub-folder of your remote site so that you maintain a one-to-one relationship of the structures both local and remote.