First of all, check that the licenses of both QlikView Server and Publisher are all right. Go to the QEMC, System, Licenses, and click on each. If Publisher is not licensed, do it, otherwise the options mentioned below will not be available.
If they are ok, then you will see in the System, Setup tab of the QEMC a folder named "Distribution Services", expand and select your server (should be something like QDS@servername) and under the General tab, you will find a textbox to specify the Source Folder.
Hope that helps.
Do you mean that you installed the program files to another disk on the same machine, or you installed on a new windows instance? From V10+, the QVPR folder lives under the ManagementService application folder.
For Win2003, the location is
C:\Documents and Settings\All Users\Application Data\QlikTech\ManagementService\QVPR
For Win2008, the location is