Even for an intranet, you want the files to reference the internet domain, such as
http://office.mydomain.org
You can upload files from the C: drive, but Adrian mention ExpressionEngine and probably every content management system (CMS) will expect the files to be stored in the web area
of your machine. Pointing to the generic C: drive, is pretty much like saying, these files are located on every employee's computer who attempt to use them. The C:drive is local machine reference.
You want to reference the server. This can be done by IP address, as well, but is best done by a domain name, even if its internal.
If your website is hosted elsewhere from the intranet, just call your ISP, and ask them to point a subdomain, to the IP address of the machine you are using for the intranet. Anything like, office., staff., internal., in front of your current domain name should work.
Then just place the files in a folder, within the web server area. So if your structure was like:
public_html
-- /system/
-- /images/
-- /themes/
-- /files/
The reference to the files will then become:
http://office.mydomain.org/files/{file_name}
or you can use the reference, just /files/{file_name}
If you have lots of files, I also recommend grouping them under the files
or downloads
folder. Just create sub-folders. This will make uploading files using the file manager or something like 'Assets' by Pixel & Tonic easier, when they don't have to try to display 1000s of files at a time.