The FAQ How do I keep my own module/library directory? is very relevant to your question.

Basically you pass PREFIX=/the/directory/you/keep/your/modules/in to Makefile.PL (you can make the CPAN module do this by typing o conf makepl_arg PREFIX=... at its prompt (presuming you're using perl -MCPAN -e shell or similar)). And to make your scripts atuomatically use your copy of the module you can put a use lib at the top of your script, or set the PERL5LIB environment variable to tell perl to look at your directory first (see perlrun on that).