SH3 Commander is a seperate application, external, that you launch befor SH3.
SH3 commander should not be in your mods directory. Use the exe to install it.
You can use JSGME to enable GW. You have it in the correct location, the mods directory. When you do enable it, it may take a few minutes before it finishes. (It's working with a couple Gb of data.)
The .exe for GW is just a file extractor. You can type in a path other than the default SH3 directory and manage the files just like any other mod.
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