Commission arrangements must be in writing in California. Whether calculating the commission after subtraction of the merchant fee for a credit card transaction is permissible will depend on how your commission plan is written. Consult with an employment lawyer.
This sounds like a use-it-or-lose-it policy, which is not permitted under California law. The company can set a maximum vacation accrual cap over which employees cannot continue to accrue vacation leave. But once employees accrue vacation, it cannot later be taken away. (There are sometimes exceptions in a union environment with a collective bargaining agreement that provides a different method.)