Main Usage is to convert the character set of your database content.
After you get vCC installed, it will tell you about your settings, if you see them wrong, then it gives you a link to update them.
You can access the converter via the new link at the sidebar in you ACP.
If you have MySQL 4.1 or greater you have to choose a collation that match your desired character set. this usage includes the secondary one as a default step.

Secondary Usage is to convert the collation of the database only, without touching the content, this is valuable for those who converted using a previous version of vCC which didn’t support collation converting, or for those who installed their vBulletin forums but they didn’t care about the collation. This usage is a default step in the main usage.
To have your database collation only converted, you have to set that in the settings.