Working with Custom Upload DIrs

Hello. To get the 2005 version of life, and to enable media library to be saved in “custom upload dir” with a plugin of the same name (based on our permalink paths) it seems S3 Media Offload doesn’t play well. It takes over and insists on the Year/Month URLs, or URLs with no folder structure at all. Any ideas on how to make this work? I’d like to be able to upload our files to S3, and use the CDN as I do, but with the benefit of proper folder structure. Any ideas? Thanks.