I suggest you have a close look at how the IndigoPerl installer does the installation / setup of IndigoPerl. They create links to Apache in the Start Menu.

For the name and location of the special system folders, you could either dig in the registry for the keys that hold these values (Win32::TieRegistry would be a good module) or you could use the appropriate Win32 system calls (Win32::API is the module for that).