With great care.

Seriously though - this is hard to answer without knowing what kind of connection to the database you have. If it's on a hosted web server you most likely only have access to it through PHPMyAdmin or a similar tool.

If it's your own server you can use pretty much any type of tool to connect to the database to perform maintenance tasks.

The most important thing to take care of, if your site is of any value to you, is backin up the database. If your web host doesn't back up your database then you need to do it manually. How to do this also differs depending on what access you have to the host.

PHPMyAdmin has functions that allows you to backup an entire database. It's a bit cumbersome to do it this way but it's a lot better than nothing.

Otherwise you shouldn't need to fiddle with the XOOPS database on your own, the admin interface takes care of that.