Replying to comments on your puzzle

[Merdock]

Is there a way to reply to comments on your puzzle, besides making a general comment

[jessica6]

If you are the author, you can "edit" comments made on your puzzles, even if the comments are not your own. You may also hide or un-hide specific comments.
Be aware if you make an own hidden comment (not editing), the addressee can't read it unless he/she has solved the puzzle.

So what you can do is add a reply like "Merdock: <your reply>" at the end of the comment you want to reply to.
Or you can make a general (non-hidden) comment like "@commenter: <your reply>", but be aware not to give spoilers because everyone can read these comments.
Or you can send a PN in this forum, if you know the commenter's nick here.
Usually authors will use the first option (editing comments). On another puzzle website (croco-puzzle, not existent anymore) there was a direct option to reply to comments, which meant the comments were organized as threads.

[uvo]

If you are the author, you can "edit" comments made on your puzzles, even if the comments are not your own.

You can, but unless you have a good reason to do so, you shouldn't. If you simply wish to reply, write a comment under your own name.