If you are comfortable with Content types then you can associate the workflows with the content types - the new button will allow the user to choose from one of the two content types, each with the appropriate workflow.
Otherwise, if you are not comforatable with content types and you are willing to copy items between lists using SharePoint designer, you could create 3 separate libraries, two of which host the workflows and the other to receive the approved documents. When your users begin authoring or uploading documents, direct the user to to two workflow lists upfront each with the appropriate workflow associated with it. From there you could trigger the workflow and, upon approval a simple SharePoint Designer copy list item workflow could copy the approved item to the ultimate target list.