How to archive mail with Mail.app?

i just create a saved mail folder and drag the emails i want to save into there.

Instead of archiving all your mail in a single “Archive” mailbox, you could create multiple mailboxes for different topics, route incoming mail there according to some criteria that junk mail wouldn’t satisfy (such as who sent them), and manually move to the appropriate mailbox any messages that remain in Inbox.

There is no need to copy the messages instead of moving them, nor to mark them unread. You can just move your mail wherever you want it to be permanently stored and set up a smart mailbox that shows unread messages only.

And if you really want the junk filter to be evaluated first instead of last, go to Preferences > Junk Mail > Advanced, take note of how the junk filter rule is defined (you can make a screen shot of it), set up a custom rule that does exactly the same, and place it above the other rules. Assuming the junk filter is in Automatic mode (i.e. junk mail is moved to Junk), all incoming messages that don't satisfy the criteria of this rule (i.e. that aren’t junk) will be processed by the rest of the rules.

You’re welcome.

What determines the update of a "Smart Mailbox"?
Do I need to click away and click back?

Yes, you must do something like that for messages to disappear from the smart mailbox after reading them, but you don’t have to click on another mailbox if you don’t want to. You can just Command-click (⌘-click) on the smart mailbox to unselect it, then click on it again.

Note also that newly arrived messages will show up in the smart mailbox automatically without you having to do anything.

how do you suggest I indicate that I've completed/resolved
an email/TODO item?

Well, I guess you’ll have to change habits and decide for each message whether you want to keep it or not. If you want to keep it, either do nothing if it’s already in the appropriate mailbox, or manually move it to the appropriate mailbox if it isn’t.

It may take some time getting used to it and you may end up accidentally deleting some messages, so make sure you choose the right Preferences > Accounts > Mailbox Behaviors > Trash settings... 🙂