Which way will the FTP conflict fail?
The article you linked to describes the nature of the conflict in detail.
cPanel users? Or Centova users? Or both?
Whichever one starts first will "win".
Should I select Pro or Pure FTP when doing so?
If you're running a separate FTP server for your other control panel, it doesn't matter. If you're using v2.x integration, you'd have to use Pure-FTPd. If you're disabling your CPanel FTP server, then it's irrelevant.