SH3 Commander is a stand alone mod, and doesn’t need to be in your game JSGME.
You have to extract GWX files to your SH3 installation and it can’t be in your game JSGME.
ARB Wide Gui have to be dropped in your game MOD folder, then activated via your game JSGME (assuming you have already installed JSGME to your game folder)
PS: ARB have a SH3 Commander folder inside that need to be pasted in your SH3 Commander!