Ok...assuming I read that all correctly:
You do not need Cron Jobs. You Will need to create a script that will break down your file and then execute the proper queries to insert into the database.
You will then upload that file, and whatever file you have been uploading via your website, via FTP.
Then execute the script in the browser. I would recommend having the execution page password protected and allow user input for the files names. So you can upload 50 files, then enter 50 names and execute the command all at once.
Hope that helps and makes sense.
🙂