You don't.

More properly, you can change your profile (~/.bash_profile on 10.3+ by default, as I recall) to cd upon login from your home dir ~ (/Users/Name) to ~/directory, but that's very un-unixy.

Why don't you work on your scripts, and when they're as you want, do:

$ mkdir ~/bin
$ mv perlfile.pl ~/bin/
$ chmod +x ~/bin/perlfile.pl
[download]

... and then edit your .bash_profile or .bashrc to add ~/bin to your PATH?