best way is to have actual tree inside folder (c:\bla-bla\patches\my-super-patch\source\usr
c:\bla-bla\patches\my-super-patch\source\usr\share
etc.)
and use git in commandline or any tool, init folder and commit original files, and then you only need to produce git diff to file and output will be your final patch you can test in patchmanager directly.