If you have successfully installed GWX over your stock SH3 game, you don't have to do anything to enable it. It's there, baby!
If you're talking about the optional GWX mods in your new MODS folder, there is detailed info on all of them in your GWX user manual.
Personally I won't sail without Integrated Orders. I also like the Enhanced Damage mod, and used the 16K Atmosphere mod before I started experimenting with environmental mods from other sources.
Be aware, though, that some of those mods - the 16K Atmo, for instance - will increase the demands on your system. The basic GWX install was specifically designed with the original SH3 system specs in mind, but that's not necessarily the case with optional mods that come with it (or any other mods, for that matter).
Which is why you should read about them in the manual to see which ones you want, and then experiment to see which ones you like and which ones don't overload your rig (if that's an issue you're even concerned about).
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