Working with Watch Folders - Eliminating Source Folder

I am trying to setup an automated proxy workflow with Media Encoder in which I ingest footage into preset watch folders and it creates proxies for an overseas editor. 

Now, is there a way of getting Media Encoder to convert the original files into proxies without creating the "Source" folder? It would be a lot better to have the source files stay in the same location rather than in subfolders.

Thank you all for your help.

Cheers,

Javier.