You should end up with two folders to enable with JSGME:
1. Supplement to V16B1 (JSGME) - h.sie's stuff
2. Stiebler4B_Additional_files_V16B1 - Stiebler's stuff
each containing his patched sh3.exe + the added / modified mod files
Second folder overrides the files of first folder when enabled.
This is h.sie's folder should look:
This is Stieblers folder should look