When you want to archive, turn on the extra filters, select all in any folder, and use "Message->Apply Rules to Selection".
I'm sure there are more elegant ways, but this works for me with about 10,000 archived messages...
ANother ideas is you can create subfolders in Mail.app. Drag messages into the subfolders. You could make a folder for every 6 months of archives, or something. That would make searching more manageable.
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