Welcome aboard Swab! Yes, you can install both versions. I think you just have to rename on of them. Anyway, vanilla version you will tire of quickly so I recommend just going for the GWX modded version. I do not use SH3 commander so I can not help you with that. When you do get set up go get the torpedo damage mod. It is really nice. You can find it on the SH3 mod forums. Any questions do not hesitate to ask!

See you in the Atlantic....leave the crabs home though