The desktop version puts the qvf in
If you have the server version they are stored in
You can change this location in the QMC Engine - Apps tab.
I think that there is a config file on the Desktop version that you can update to change the location. But I can't remember where it is.
I am using the desktop version.
What is your strategy if you create a more complex file folder structure when you go from source data to presentation apps? In QV people easily create a tree of file folders and use variables to navigate in the script to the various locations.
BTW, I found an engine API Explorer but there is no direct way to define the location of folders.