Your employer's efforts to force you to accept cash to avoid paying you overtime is against the law. I would need more facts to identify any additional violations, but it seems to me that he is not providing you with accurate pays stubs if he is paying in cash, he probably does not give you or others the opportunity to take your meal and rest breaks, etc. Your legal rights are being violated and you should contact legal counsel to discuss pursuing your claim(s).
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Your employer is not able to avoid the minimum wage laws of the state by simply characterizing your job as a flat rate job. You have a couple of options available to you. One is to make a claim right now for the money you are owed for the work already performed, with the hope that the employer will change its practice in the future and pay you correctly. To make a claim you can either file a small claims action, file an administrative claim with the Labor Commissioner's Office (also known as the Division of Labor Standards Enforcement) or hiring an attorney a suing in superior court.
Alternatively, you can continue to work, keeping track of all the money you should have been paid and the hours you have worked, and later make a claim, after you have found another job. The advantage of this approach is that you are not subjected to any kind of unlawful retaliation if you wait to make a claim until after you have another job. The disadvantage of this approach is that the longer you wait to make the claim, the larger obligation to repay becomes, and you might get to a point where you bankrupt the employer and don't get the money anyway.
Good luck to you.
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Your employer is required to pay you overtime if you work more than 8 hours in one day. Even if you both agree to your employer's demands, you cannot lawfully waive your right to overtime pay. Based on the facts you provided, you likely have a claim against your employer for failing to pay you overtime. As my colleagues mentioned, it sounds like you also have other potential claims so consult with an attorney to discuss specifics. If you file a claim now and your employer fires you because of it, you may also have a claim for retaliation.
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If you work overtime and are nonexempt, you are entitled to time and one-half for hours worked over 8 in a day OR 40 in a week and double time for over 12 hours in one day. If you work 7 consecutive days in a workweek, you are entitled to time and one-half the first 8 hours and double time after that. If you refuse to work without being paid overtime or assert your right to overtime and are retaliated against, you may have additional claims for unlawful retaliation and/or wrongful termination. You are wise to assert your right to overtime pay and the statute of limitations (deadine to sue) is 3 years and sometimes 4 years.