[jputnam]

Well, I figured it out. :D

Using OS X Server Admin, Workgroup Manager and the Finder:

1. In the Finder create a new folder/directory in WebDocuments (I called it "omni".)
2. Again in the Finder create a new folder/directory for each omnifocus user inside the "omni" folder/directory.
3. In Workgroup Manager create a new Group called "omni" and put your omnifocus users in the Group.
4. In Server Admin go to File Sharing, go to the new "omni" folder/directory. In the Permissions window, add the Group “omni” and set the permissions to Read & Write and set the permissions on “-www” to Read & Write. Save.
5. Still in File Sharing Permissions, select each user’s folder/directory in turn, add the user to permissions for each corresponding folder/directory and set the permission to Read & Write for the user and Save and for -www and Save.

That’s it. Now users can sync to https://<server>/omni/<username>/

They’ll need their server username and password to authenticate.

Doing all this worked for me. I hope it helps someone else.