If I was writing an application with perl where should I put the files?

I take it your Perl "application" is one or more Perl scripts, and a suite of modules. There are standard places where these go for installing as root (if you're not installing as root, this can be done - you set up your own custom directory tree with bin lib and man directories, and include lib and bin in PERL5LIB and PATH respectively).

The default place to install will be the same directory tree as where perl itself is located, usually /usr/bin/perl or /usr/local/bin/perl. If you are using a standard install (by root) you won't need to know exactly where modules go under /usr/lib or /usr/share, as this is taken care of for you.

Hope this helps