The Database Properties, second tab, %used is not related to your mail quota. It is related to the amount of whitespace in your mailfile.
If you delete a bunch of emails and then check your %used, you will find a much lower %. That is because you have expanded the mailfile to accomodate those messages, and then having deleted them, there is room left in the file. (It is kindof like a balloon that has been blown up and then the air let out.) If you then run a compact against your mailfile, it will recover all the whitespace, and the %used will be much closer to 99%.