Smart Mailbox questions

Each Gmail label can be assigned to a MailMate tag in the Tags preferences pane. If you have that then you should be able to use the “Tags/Keywords” condition to match messages without the label.

Excluding mailboxes should be possible using the “None of” operator in the “Mailboxes” pane of the smart mailbox editor. Something like this:

All
    Mailbox A
    None
        Mailbox B
        Mailbox C

That would match any messages in A which are not in B or C.

Alternatively, you can use conditions like this:

Source ▸ Path is not “Some/Specific/Mailbox/Path”

I hope that answers your question.