Ah! I did not know it was version 6. There is upgrade instructions available in the Online Docs, but it's basically backup your current install, erase your install (rename the folder is a quick way), install the new version, restore your customized files (theme, templates) and the config files (config.inc.php, license.php).
As for converting your flat-file database to the mySQL, you will need to send me your flat-file, and I will send you back a .sql file that you can import into the table. Use the link in my signature.
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