What permissions do you want to set? If you want to set a canned ACL with the upload, you can either set it in the web.config (if it applies to all uploads), or inherit a custom upload stream provider from S3UploadStreamProvider and override the CreateBlobInfo method (if you want to set different ACL's for different uploads).

If you want to set a more detailed access policy than a canned ACL, you'd need to use a different component to set that after the upload -- SlickUpload doesn't currently support setting advanced ACL's.

To do the config in web.config, add the cannedAcl attribute to the uploadStreamProvider configuration (see the docs: http://krystalware.com/slickupload/documentation/configuration).