Nope.
When you downloaded GWX and installed it a handy utility was added to you SH3 Program folder. The JScones Generic Mod Enabler (JSGME). You will find a JSGME.exe inside the program folder. When you are docked in port before/after a patrol run the exe to create a MODS folder & to open the interface menu of JSGME.
All JSGME ready mods can be placed into the MODS folder and enabled via JSGME's menu. FYI there are allready some really cool extra mods bundled with GWX.
What JSGME does is to enable your added mods while making a backup of the original files which will be affected when you enable the mod of your choice. This means that when you disable your mods you
should have a clean unmodded base version of SH3/GWX.
There are some basic rules to enabling mods via JSGME:
1)Be docked at port before/after a patrol.
2)
ALWAYS rollback SH3Commander (if using) before enabling/disabling any mod.
3)NEVER delete the backup folder.
4)Enable/Disable your mods in the JSGME menu
5)Restart your game by either the SH3 shortcut or via SH3Cmdr.
JSGME will even tell you when one mod is going to affect another.
To use JSGME you need to make sure the folder structure is correct after the extraction process.
JSGME ready mods should have the same structure as below:
Positive Bouyancy Mod > data > etc etc
Sometimes after the extraction process you are left with an extra folder, like this:
Positive Bouyancy Mod > Positive Bouyancy Mod > data > etc etc
Keep you eye out for this.