Thank you for being patient with me in the explanation. Hopefully I can clear up some confusion.
First, the bc_desktop is no different than any other app. It will still have all the same files and structure. In fact, any app you develop for OOD must have that specific structure with those specific file names as they are known to OOD and will be picked up for their various functions: manifest.yml for app metadata, form.yml for the form, template dir for the scripts to launch your app on the backend, etc. So This app is no different than any other.
I think the simple thing here is to just tell this sandbox app to look in the same location your system app is defaulting to with the submit attr in the doc I shared for Custom Job Submissions.