You can put the scripts wherever you like on your system. However, the location should be in your PATH environmental variable, or you'll have to type the complete path to your file.
In addition, you need to make sure the files have execute permissions and that they include the shebang line as the first line (#!/usr/bin/perl) in the file.
Once you've done that, you type perl scriptname.pl on the command line in the terminal. That's all you need. :)
HTH,
/Larry
Update: Fixed a couple of typos. :)
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