In CPT not concrete games, but just positions and moves are saved – independent of any games. Of course, with this information it’s possible to re-calculate a move order to reach a certain position, but in general the approach is very different to typical chess databases, because the goal of CPT is quite different too. So, please unlearn to think in terms of games for the opening repertoire module.
One major difference of a position database is that the program covers transpositions within the same opening or across openings (even repertoires). Especially with openings which transpose quite often you will soon appreciate this feature. Every position and move is unique in the database. The same position or move (for a certain position) is never saved twice. If you add a comment to a position or move and it is part of two openings it will be shown for both openings the same. If you edit the comment for one opening the updated comment is shown for the other opening. The same is true for position or move evaluation or training result. However, you can decide to exclude a move for a given position for an opening. For example you might play the Closed Sicilian for both sides. Then you are not forced to maintain all moves for both sides. Instead you will most likely have for the opposite color all possible replies and for your side just one. Also you can have different rankings of your candidate moves per opening.