This is not really a tax question, but more of an employment law question, so you would get your best answer from an employment law attorney.
One thing you should do when you get your W-2 is make sure that your employer did not include in your wages the fees he kept for the credit card fees. If he did, you can request that he issues you a new W-2. If he is not willing to, then you can file a complaint with the IRS so you are not paying taxes on money you did not receive. Instruction on how to file a complaint are in this link. Call the IRS at 800-829-1040 or contact your local taxpayer advocate office to help with a complaint.
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