Create and manage a custon table in an extension: How to
Check this section on the wiki: https://wiki.civicrm.org/confluence/display/CRMDOC/Create+a+Module+Extension#CreateaModuleExtension-Addadatabaseupgrader/Installer/uninstaller
You will need to add an upgrader to your extension, and from that upgrader you can manage your database file installs. Also, you might want to add a DAO class?