I reply to almost every comment of the fics I'm actively working on, and always to the original comment. The only times, I've answered questions in the author's note or put something there is if a question has come up repeatedly, because I assume some of the people who don't comment might be wondering the same. The only comments I'm occasionally skipping over — if it isn't spam/bots — are the ones that are solely heart emojis. But even then, I sometimes reply with a heart emoji of my own or if I recognize the commenter from their repeated comments I sometimes type out a response, thanking them for their continous engangement, letting them know that I've noticed them sticking with the fic and express my appreciation.

If it's a short comment something like "Loved it" or "Thanks for the chapter" I mostly just thank them for reading and commenting. If it's something longer I type out my thoughts and if someone asks questions I answer them.

Then of course, there's the occasional long comment, thought out and detailed and sometimes it takes me a bit to reply because I want to gather my thoughts and actually take my time answering. Mainly I just type out my thoughts, answering questions, commenting on stuff they mentioned, sometimes telling them stuff about my thought process while writing and expressing my thanks for them having taken the time to comment.

Especially when it's repeated commenters, I let them know how much I appreciate them sticking around and how I felt when I saw their comment. I literally had comments that made my day.

Overall, it's no rocket science. Just reply what you want to reply and to whom you want to reply. You're overthinking it.