You are close! The second workbook, where you connected to the Tableau Server Data Source, is just a connection to the metadata. In that workbook you can perform data blending, add calculated fields, etc but it is all local to that particular workbook.
If you want to edit the actual data source, you will need to re-connect to your original data source in Desktop -- not the one on Server. Then you can make your changes and re-publish it to the Server.
After re-publishing you can simply refresh the second workbook to pick up the changes.
Does that help?
Ooohhh!! SWEET! Yeah, so I went back to the original data source and added a new custom metric. Then I went back to the second workbook and refershed it ... Vuala! There was my new metric. Cool. Yeah, I was under the assumption that I could modify the data source and save the changes when not operating in the original. Good to know.
Thanks for your quick response and help, Tim!