On the "Edit User Settings" page (in the menu when you click on your username in the top right), there are "Notifications for Comments on My Posts" and "Notifications For Replies to My Comments" checkboxes—one would hope that, as long as those are checked, the bell should give you notifications when people reply?
This is correct.
We did not port over all of your old notifications, and from looking through Document's posts, it seems like they shouldn't have received any comment notifications since the relaunch, so my guess is they are looking for all the historical notifications, which I will sadly have to admit are no longer accessible in the same way (though importing them is definitely a possibility if enough people care, it just wasn't on our list of priorities and we've never gotten any request for them so far).
On the old site (like on Reddit), there was an envelope in the upper right that led to all replies I'd received to my posts and comments. Now there's a bell; but all its tabs currently say "You don't have any notifications yet!". What am I missing?