Feel free to play around with the configuration, BUT be sure you have a backup, or are working on a test system! You'll find the X-Dedupe system in the "Administration" menu under "Automation".
Ideally you would already have a specific case in mind. Maybe there's something that you could not get to work with the built-in deduplication? Or was always too slow?
Can you get the configuration into a status where you feel it's failsafe? All the manual cases look fine? So go ahead, make a DB backup, and run it. Let's see what happens.
There is this one thing that doesn't get resolved properly? This one attribute that you need, in order to identify the candidates for being duplicates. You can simply create your own modules, see here, and it's not even that difficult.