Sounds like you hit the Clean up your Bags icon on the main bag. I haven’t tried it in awhile but I think it works like a toggle. It won’t reset your existing items back to where they were, you’ll have to do that manually, but you can click it again and move all your stuff back. New items should go into the bags properly.
You can also designate each bag to carry a certain thing if you want. That’s an icon at the top left of each bag’s window.