Why not - instead of fully qualified path-names you can use %ROOT% (the parent-folder of you WPI-folder) for example .
e.g.
CODE
your_cd_root
WPI
...
WPI.exe
Apps
YourApp
setup.exe
In WPI you can now define your setup-command like this:
CODE
%ROOT%\Apps\YourApp\setup.exe /s
Al