This is a tough question to answer since it's so general. Normally you don't need to modify any content what so ever outside of the XOOPS admin interface and the actual site you're running.

If you for some reason need to hack into the XOOPS database there are numerous ways to do this. Some web hosts only allow PHPMyAdmin, other grant you shell (telnet or ssh) access and access to the MySQL client.

If you are running your own setup you might be able to connect with MySQL Control Center or any other MySQL management tool available.

You can write your own PHP-scripts and upload them via FTP that hacks directly into the XOOPS database and updates whatever it is you think needs updating.

You should never need to do any of this if your XOOPS installation is set up properly though.