Assuming you want to scan all of these subfolder (in QVW and QVD), you can point to both in the "List of File Paths to Scan" in one of two ways:
1) Use C:\QV --> this will scan all subfolders and files
2) Use C:\QV\QVD in box 1 and C:\QV\QVW in box 2 (same as above)
If you are only wanting to scan a subset of subfolders in \QVW or \QVD, then you can use the "Excluded Files | Directories" search terms (as noted in the online help documentation) to exclude certain subfolders.
If neither of these options work, consider using the Multi-Cluster support option in GovDB 1.1, again, as described in the online documentation http://documentation.qlikview.com/governance-dashboard/1.1/QlikView_help.htm#Create_a_MultiCluster_Script.htm
Does this help?