auto-publish document

We are using the auto-publish feature.   But we sometimes need to add the folder to a different folder than the folder specified in the publish path.   The user is uploading the document to document manger, then attaching the documents to the record.  The auto-publish feature is then publishing the document a second time to the document path.  I thought that  a document would not be published to DM if it had already been published. Is there a way to keep the attachments from publishing on individual records?