In modbuddy, go to Tools->Options->Civilisation Beyond Earth.
You'll see two text boxes to enter file locations in.
In "Use Custom Civilisation Beyond Earth Path" put the location where the game is installed (e.g. C:\Program Files\Games\Steam\SteamApps\common\Sid Meier's Civilization Beyond Earth)
In "Use Custom Civilisation BE User Path" put the location where the game stores your saves, mods, and other user data (e.g. C:\Users\User\Documents\My Games\Sid Meier's Civilization Beyond Earth)