Running a WP Repair Tool, what to do first?

I have received this message on my WP site:

To allow use of this page to automatically repair database problems, please add the following line to your wp-config.php file. Once this line is added to your config, reload this page.
define('WP_ALLOW_REPAIR', true);

I can do this. I have my config file downloaded via ftp and added code it, but am wondering, before I run that repair tool, if there is anything I should do first. Is there anything via FTP I can backup for MySQL before I do this?

The site has been having lots of flickering going on and off and Internal 500 errors. I was even trying to hire someone to find out what the issue could be (hosting at hostgator, I have a VPS) when this occurred.

It makes me nervous to run it. Advice?