On our systems, we use an /appl heirarchy for major projects. Thus, with a well-defined project might have some or all of these:

/appl/project/bin      main program stuff for 'project'
/appl/project/etc      configuration
/appl/project/var      state information
/appl/project/tmp      temporary files (maybe use /tmp?)
/appl/project/lib      libraries, modules, etc.
/appl/project/doc      developer and minimal usage docs
[download]

Not all of these are particularly necessary (especially if the project is small, in which case none of them necessarily are). Sometimes this makes module installation more straightforward if they have specific needs and don't necessarily want the module installed publicly or getting the SA to do it is too much trouble or time. Just tell CPAN that the prefix is /appl/project, and use lib '/appl/project/lib';