If your as crazy as me then just overwrite the files directly into your data folder.
So mod fix data folder copy paste to your installed game data folder.
Bingo..
Then just use JSGME traditionally for the regular mods already installed.
GWX 3.0 will be updated.
Problem is if GWX team comes out with a patch 3.1 then we're screwed... sorta...
So only if your as crazy as me you should attempt this. Otherwise follow as best as possible as the instruction say.
But as I said I'm crazy so I don't read manuals... I like trial and error better....