No. GWX 2 should direct itself to the main SH3 folder. Since it self-installs, it knows where it should go. Just let it do its thing, and you'll be good to go.
As for JSGME to install normal mods:
1) Create a desktop icon linked to the JSGME installed in SH3 (I have one for SH3, one for SH4 and one for SH3 Commander).
2) Open it from the icon and you will see that JSGME has all the mods stored on the left-hand side. Click the arrow to move a mod to the right side, which activates it.
3) If you decide to remove a mod, click the arrow which moves it back to the left side. It remembers what it did and will automatically take care of changing the files back and forth.
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