You’ll need to write/update a custom collector to identify what the source files are, and then add some logic to define what the destination template should be for each source file type. Then you’ll need to verify you have the necessary fields to build the destination path from the template.
To do all this you’ll have to parse the source filenames (if they don’t follow a SG template) or use template_from_path.
Basically; custom collector, and/or custom plugin.