Ah, right. The only thing to be wary of is that the Spy Sat mod contains a campaign layer from the version of SH3 that you are using. So Spy Sat must be installed while in port and docked. As for SH3 Gen, this mod will work after Spy Sat has been enabled. SH3 Gen only reads from your save game so thee should be no conflict.
But it sounds as if your up & running. Happy Hunting
