We're working on a full set of instructions, bu tin the meantime:
Uninstall SH3 fully & delete the SH3 folder in My Documents.
Reinstall SH3 and patch it to 1.4b (may already be patched to 1.4b, depends on your copy)
With all the GWX 2.0 downloaded files in a folder together, run the GWX.exe installer and point it to your SH3 installation.
That's it your done.