If you are using qlikview Server SR1 with server and publisher.
first let me conform that how many tab's you see in Documents tab of qlik view server.
If you see two sub tabs by name Sourse document and user documents this means you have publisher.
if you only have User document then it says that you don't have publisher license.
Scenerio only server
If you have server without publisher then in document's tab you will find only one sub tab by name users documents.
here is the place you do scheduling and all.
But I believe you have publisher even.
Scenerio server with publisher
If you have this case then in document tab you will find two sub tabs by name sourse document and user document.
and if you go to user documents and try to reload document or schedule task you cannot do this from here.
you can schedule documents which are there in sourse tab only.
In order to acheive this.
go to wemc --> systems tab --> setup --> management service --> distribution service --> expand it and select qds@server --> go to general tab here you will find application data folder section. Point this to you project directory where your applications are present.
and even change the location of qlikvies server folder to pint to some new folder.
Hope this helps
If you have still more clarification then feel free to ask