Mac Mail archive folder when used with Gmail

I use Mac Mail with a Gmail based account. I recently figured out that the Archive button in Mac Mail wasn't working, and it turned out that the archive folder was configured to point at something that didn't exist (unclear why). I "fixed" that so that it now points at Gmail's All Mail folder. And now my Archive button behaves as I would expect.

However - now every time I search I get messages in the Archive folder, which I guess I understand, but I have also saved many(!) years' worth of messages in specific folders for organization and search used to find them in those folders - which was better because I could quickly see context by seeing which folder I had saved something in. Now everything search finds is in the Archive folder.

Anyone have a suggested workaround for this? It seems like I can either make the Archive button work or make the search work how I want, but maybe not both.

I also understand and sometimes use the Gmail web interface for max flexibility, but for quick and easy I'd rather just stay in Mac Mail and have it "mostly" work.

Thanks for any insights.