if you want your user to be able to retrieve you documents by searching with metadata and not just the files content, you have to import the files into document  libraries, and don't forget that it is not a good mractice to have content db > 100 - 200 GB; you may have to split it up into several site collections ->several content db.
-Otherwise, if you don't want to leverage metadata in search (which I doubt), keep the files in the shared  drive.

1°First off, read lambert Qin's answer.
2°if you have several top level web site as indicated in your post
<<
i've already built multiple top level site on http://mossdev01:10001/ namely:

http://mossdev01:10001/sites/PMO/default.aspx
http://mossdev01:10001/sites/ProjectA/default.aspx
http://mossdev01:10001/sites/ProjectB/default.aspx
http://mossdev01:10001/sites/ProjectN/default.aspx
>>

Each top level web site is the root site of a site collection, ->you have several site collections
You can read this article from Technet :

technet.microsoft.com/en-us/library/cc825782(office.12).aspx

if you want your user to be able to retrieve you documents by searching with metadata and not just the files content, you have to import the files into document  libraries, and don't forget that it is not a good mractice to have content db > 100 - 200 GB; you may have to split it up into several site collections ->several content db.
-Otherwise, if you don't want to leverage metadata in search (which I doubt), keep the files in the shared  drive.