I'll assume that in the Publisher ControlPanel, you have defined an AccessPoinr Resource and have built Distribution tasks to distribute documents to that Resource.
The remaining task is to edit :
C:\Documents and Settings\All Users\Application Data\QlikTech\Publisher\AccesspointService\Settings.xml
and create an <AddDirectory> element that points to your AccessPoint directory.
By default, the QVS directories are included in AccessPoint. If you want to exclude them, create a <DenyDirectory> element in Settings.xml. Comments in the file provide instructions for creating both the AddDirecory and DenyDirectory elements.