"She receives both cash and credit card tips that she's told to "skim out of the cash drawer" when the customer includes them"
The problem with that is, if the employer gets upset with her for any reason, he can charge her with embezzling, and she could be hard pressed to prove otherwise. By law, the employer is required to withhold taxes on tips received by an employee.
Please read all at https://www.irs.com/articles/reporting-tip-income-irs to see what actions she needs to take as an employee to cover herself on the legal front.
Then I would suggest she update her W-4 with the employer to increase the tax withholding on each paycheck, so you don't get hit with underpayment penalties at tax time when she does report the tips on your joint 1040 tax return.