You are correct. The native quota software only works for the entire drive. So for example you can setup the quota management so that user Bob can save only 5 Gigs of data to the server’s drive. If you need to do quota management at a finer level you will need third party software.
Some examples are: (You’ll need to determine usability in your environment)
<a href=”http://www.advancedtoolware.com/software/disk-quota/disk-quota.asp”>SpaceGuard SRM</a>
<a href=”http://quotaserver.it/”>Northern Quota Server</a>
<a href=”http://www.symantec.com/redirects/veritas/veritas_com/storageexec/”>VERITAS StorageCentral, formerly Precise/StorageCentral SRM</a>