Yes, you should assume that the moderators will know, and you should be fine with them knowing, because you’re not using the multiple accounts to escape moderation, but rather for greater anonymity in the comment thread.
The rules that I follow, which I think are implicit in “use good judgment”:
1. Don’t vote on the same thing from multiple accounts.
2. Don’t participate in the same comment thread with multiple accounts (or if you do, only separate parts of the thread). Don’t create a fake impression of consensus or have your accounts interact with each other.
Those are probably the two big ones I would imagine.
Whether the accounts are actually tied together on the backend, I don’t know. I would suspect that they are not automatically linked, but could probably be linked if the moderators are investigating you for bad behavior (like voting on the same thing with multiple accounts).