Weever works with EE's built-in comment module. Most of the work is done by the extension. However, although the extension can get us 95% of the way, we need the plugin to finish up for us. In your template, wrap the Weever plugin around the comment module tags:
{exp:weever}
{exp:comment:entries}
{/exp:comment:entries}
{/exp:weever}
Weever is not a replacement for the Comment Module. Instead, Weever works "on top" of the Comment Module. Replacing the Comment Module would have required replicating all of its features -- no small task, to be sure. If you need a brand new comment module, this isn't it. Weever works by letting the Comment Module do its thing -- determine who has permission to see what, fetch information from the database, clean it up for display, and so on. Meanwhile, Weever takes the Comment Module's data and modifies it, creates a bunch of new variables, wraps the comments in some helpful containers (for CSS styling), and gives it to the user.
If a comment that has replies is closed or deleted, what happens to the replies? If a comment is closed, its replies remain visible and properly nested. Depending on how you lay out the comments on your page, you may want to use the comment_closed variable pair to display a note (i.e. "This comment has been removed.") instead of just leaving a blank spot. If a comment is deleted, its entire "branch" is deleted. In other words, that comment and all of its replies (and their replies, etc.) will be deleted and removed from the database.