Here is a tip for you: You can predefine all the correct file locations by editing an ini file.
Navigate to your new deployment, find the "Revit Building" folder inside the "Revit Setup" folder within the "Admin Image" folder. There you will find a file named Revit.ini. This file gets copied to your hard drive's program folder when the deployment is run, so make your standard changes to this file prior to pushing your installs.
You can predefine the file locations by adding them to this ini file. Find the strings between [Directories] and [Design Pane] and edit them to point at your company standard folders.
Library=\\BIM\apps\Data\Office Library\RAC 2008\Content\Imperial Library, Metric
Library=\\BIM\apps\Data\Office Library\RAC 2008\Content\Metric Library, Imperial
Detail Library=\\Bim\apps\Data\Office Library\RAC 2008\Content\Imperial
Library\Detail Components, Metric Detail Library=\\BIM\apps\Data\Office
Library\RAC 2008\Content\Metric Library\Detail Components, Training
Files=\\Bim\apps\Data\Office Library\RAC 2008\Content\Training, Haskell
Library\Haskell Standards\Shared Parameters\Issue_Date.txt
This will keep all your users accessing a consistent set of standard files.
Note: The installer doesn't appear to overwrite an existing Revit.ini file in that same location, so be sure to uninstall the previous build or rename this file prior to running the new deployment.