in reply to Perl software on multiple files
Your questions give little support to your statement that you're "a perl coder since some years" because at least one generic answer to question 1 is "write modules." The answer to question 2 may depend on the OS, tasks and user skills. Searching on terms such as "background process" "Input loops" and the like may provide illumination; lack of a GUI is no bar to anything you've described, but the description is less than complete, precise or even coherent.
Otherwise, you'll need to refine your question -- preferably with code and data as it stands if and when you become stuck.
How do I post a question effectively? will enhance your skills at asking a question here; you'll also find that reading other introductory information about the Monastery (in On asking for help and I know what I mean. Why don't you?) will prepare you to make it easier for us to help.
Lastly, you'll perhaps want to freshen and deepen your knowledge of Perl by reading such standard texts as Learning Perl.