- Installs are per machine, not per user, so end users would not have to change anything.
- The PDF Ownership setting should have been set during the original install either via the Wizard or the LEAVE_PDFOWNERSHIP property: http://www.adobe.com/devnet-docs/acrobatetk/tools/AdminGuide/properties.html#property-list
- You might be able to set the behavior simply by setting the default PDF handler under Edit > Preferences > General.
HTH,
Ben