You can set up a "share" (or point to an already created one) that enables Webdav for IOS devices in Server app. For example: we have 260 students that have their "home" directories listed at /Student_home. Go into Server app, select file sharing and choose the "share" that you want to enable webdav. Click the edit pencil and under Settings select Share with IOS devices (webdav). Then on your device use the URL http://your.server.com/webdav/short_user_name. If you have SSL turned on for web, you'll need https. Authenticate with the short name and password of user. This works with iPad, iPhone, Macs and Windows Desktops (windows you'll need to Map a network drive).
So Johnny Brown grabs his iPad with Pages, says get document from Webdav and is presented with the login: Enters https://myserver.com/webdav/johnnybrown for the server, johnnybrown for username and whatever for password.
You could also make a share for a group "dropbox" to share documents and such. Lots of possibilities.
I haven't messed around with the profile manager but I believe that PM will attempt to control this for each device registered to each user. If so, you'll have to enable sharing with trusted certificates in the PM. Since we're using this in an educational environment and don't have enough iPads, the students have to share which means that we can't assign one device per individual.
Hope this helps