from your question I cannot define what your real problem is.If you have multiple Shapefiles in different Windows submaps, you can select them using the Select Multiple Folders/Files option at the parameter.
Figure 1.Select Multiple Folders/Files option
In don't know how you designed the workspace you are calling in the WorkspaceRunner, but with DWG-files there is no option to Insert features into an existing DWG, so having another shapefile will probably overwrite your DWG.
If this is not the solution you are looking for, I would like to request you to eleborate a bit more on the nature of the issues you are running into.