The feature is documented as part of our larger guide on Managing a Community with Movable Type, but since it's a handy shortcut, it's worth calling out on its own. Simply point at any published comment in a comment listing page in Movable Type, and you'll see a "Reply" link appear. (If you've set your display options for that listing page to "Expanded", you'll always see a Reply link next to the Edit link.)
Click the Reply link, and a simple window will pop up with the full text of the comment you were replying to, along with a big space for you to type your reply.
As soon as you click on "Submit", your comment will be published on the relevant entry or page. If you're using threaded comments on your site, Movable Type will automatically display your comment as a child comment of the one that inspired it.
There are lots of other ways to make use of this convenient feature, but this one should be a winner if you live in the Movable Type administrative interface all day and prefer to respond to your community from that familiar environment.