Depends on your situation. If your site is younger, they may prefer comments vs discussion threads (as comments are more like G+, Facebook etc). There are USE cases for using both at the same time, but its wasn't actually designed to use both (it was designed to be flexible and to give options to admins that want choices instead of being forced to do things one way and one way only).
Some members find that the integrated discussion threads is confusing, so if thats the case, I'd try comments. The draw back is there is not any "New Comments" functionality like there is with "New Posts" within discussion threads, but they do get Alerted. You just need to figure out whats best for your specific community as no communities are the same.
One thing I'm thinking of trying out is turning the associated to thread into a "wiki" thread using the wiki thread addon. I even phrased the "Discussion" tab to wiki.
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