I have figured out what the problem is:
When I drag & drop files on "Your Program's Folder" in wyUpdate, wyUpdate then blindly installes all those files & folders under the folder containing wyUpdate.exe.
Problem is, not all my files & folder belong under the folder containing wyupdate.exe!
I have files that belong elsewhere as well...for instance:<installdir>\bin is where all my exes and other binary files are kept (including wyUpdate).<installdir>\system is where various application data files are kept.
So how can I tell wyUpdate what my directory structure looks like for my app?I have several folders which are up one level from the ".../bin" folder which contains wyUpdate.exe.