Setup help requested -- multiple domains with a master domain?

We're unsure about licensing given how we're set up -- or even how to set up correctly. I'm currently exploring the trial version and liking it very much.

We have two separate websites on our server, each with its own domain name and a folder of stuff to be protected. They are each virtual hosts with their root folders set to be subfolders of our main web documents folder, i.e.:

www.site1.com -------- documents/site1/protected_content/
www.site2.com -------- documents/site2/protected_content/

Our plan is to deploy a "master" domain name that covers BOTH of the above by having its root as the documents folder itself. That way, the protected content of www.site1.com/protected_content/ would also be accessible as the protected content of www.masterdomainname.com/site1/protected_content.

The plan is to protect the master domain name with amember, thus covering everything under one umbrella.

Is this acceptable? If we do it like this, could it cause problems using mod_rewrite? I said in another post that I think we'd be locked into using plain htpasswd protection, but I'm not sure.

Or would the following be more logical: instead of having a master domain name, just have a "site3.com" and move all the protected content to an entirely new subfolder, e.g.:

www.site1.com -------- documents/site1/unprotected_content/
www.site2.com -------- documents/site2/unprotected_content/
www.site3.com -------- documents/site3/site1's_protected_content/
-------------------------- documents/site3/site2's_protected_content/

And just have amember protect site 3's domain name.

This appeals to me but necessites monstrous reworking of site1 and site2's current pages to move protected content out and fix all the links.

Rob Beschizza