Virt-A-Mate looks for specific files in this order:
1) VAMroot/Saves/scene/default.json
2) VAMroot/Saves/scene/MeshedVR/default.json
3) VAM loads an empty scene if it finds neither of them.
The default.json in /scene/ might not be present on a fresh install but can be created by the user.
You can simply save your scene over the default.json. Maybe make a backup of the original first.