Dear Jiaheng,
Ahh. You want the order parameters for AA', AB', A'B (or, 2H, B^Mo/Mo, B^S/S).
Fair point. Only using S or Mo atoms for both layers will not distinguish between the order parameters. For example, the Order Parameters (OP) for AA' and AB' are the same. However, for the relaxed structures, the areas of these stackings are different. So, you may still be able to figure out the the stackings by looking at the OP.
Here's a simple suggestion:
If you want to distinguish between AA' and AB', you may want to use a weighted combination of Mo atoms for the Order parameters. Note that with S atoms you already are able to distinguish between A'B and the other high-symmetry stackings.
Best regards,
Indrajit