Have you tried to use your Workspace in Visual Process?
Visual Process (Page 58): http://docs.datawatch.com/datawatchserver/Datawatch_Server_v13_1_Automator_Users_Guide.pdf
In this process, you'll be able to use your Workspace.
I looked at the pdf you added as a link and it was helpful.
I did created a visual process but the workspace object give an error of "Failed to open workspace." The workspace was uploaded to the server so I don't understand how it can't open it.
Is there a tutorial or example that shows how to use a workspace in a visual process? I looked on YouTube but only found simple examples of a text file and a model. Maybe that will help.
As Chris Porthouse already stated, this has to be done via a Visual Process, but even then, you can't have the model use the 'workspace' as input. Chris was at my company doing an onsite training for Automator and the 'project' I had prepared to use in the training contained a model that used a combined table within a workspace as input. What we ended up doing was setting up a 'DataPrep Export' from the Workspace that saved to an Excel File, then I used that Excel file as input to a 'Model' and then exported the final Excel file with the Model Filter I needed applied. I tried to 'paste' a screen shot of a template I created for this and hopefully when I add this reply, it's still there. Also, as an FYI, I have 2 other Input files created in the beginning of this process that are the Input to the DW Workspace (I just didn't include that part in the screen shot).
Hope this helps,