In the 1.09 options page, I made a field for putting filetypes for exclusion.
But, for additional locations is a bit difficult I think. Actually not difficult, but if implemented - it should have been implemented from the begging... Because if I make it now, the files from uploads directory and other specified directories will be put in the same Amazon folder, all messed up.
For this to work, for every specified directory (and the default uploads dir), the plugin should have created a different folder on Amazon S3. And I think now it is a bit late, as all files are already uploaded to root dir...
Also, I don't think this will help you with the media used in your theme, as they will me max 3mb, and if that theme later will be needing an upgrade or code changes, it will be difficult to locate the media used in that theme.
But, there is another possibility, when another plugin uploads some content (like audio) to directory different from wp-content/uploads/. In that case, I think it would be better to setup that plugin to upload to a folder like wp-content/uploads/audio/ and Amazon S3 Uploads plugin will work there.