Yes, they are in different folders.
Two other questions:
1. I should be using GOLD, right, if I have both games (GLOBAL CONFLICT and GLOBAL CONFLICT GOLD).
2. One strange thing is that when I start a game and go to SCRIPTS/EVENTS LIST, there are several double entries on the list. For example, "Canadian Convoy to the UK Government in Australia" appears twice. So do several other entries. Is that a problem?