Bela can build files in subfolders, however the Bela IDE cannot show more than two levels of subfolders. It also doesn't allow to drag-drop files that should go in subfolders. So the options to copy the files to the board are to either zip them up and then drop the zip archive on the board (as long as it's < 25MB), then chose the option to decompress it as a new project, or using
rsync from a terminal on the host to copy the files over. You can also keep the files on the host, edit them with your favourite editor, then build them on the board using the
build_project.sh script, as explained here https://learn.bela.io/using-bela/technical-explainers/scripts/#build_projectsh .