First, unless the check displays the terms "full satisfaction check," or "full payment check" or similar, or the check is accompanied by a letter stating that the check is tendered in full satisfaction or full payment of a disputed debt, then your cashing the check does not operate as acceptance of the amount as payment in full for your expense reimbursement. Commercial Code 3311; Civil Code 1526.
Next, Labor Code 2802 requires that an employer indemnify its employees for all necessary expenditures incurred in the discharge of the employee's duties. So, if the check is short, then you have a fairly ironclad cause of action against the employer. The fact that the car was too expensive is irrelevant, unless you were expressly instructed not to rent a car for the amount you paid, as long as the vehicle was used within the scope of employment -- meaning that if you were out of town on employer business or required training, and you needed a car to conduct business, then you are entitled to be reimbursed. Conversely, if you were in your own community and you rented a car, just because you didn't want to use your own, then that would be your personal expense.
Re meals and entertainment, the issue is whether or not you were feeding yourself on your personal time, or you were conducting business. The former is not busines related, so your employer could avoid having to pay that bill.
Now, if you have proof that the employer agreed to cover all of your costs, then that would overrule the Labor Code entirely. But, without a written consent or authorization, what I've described above is the default.
As far as complaining to the Labor Commissioner, you can certainly do so, but hearings are running up to a year in arrears. So, if you want your money any time soon, then you'll have to sue in small claims court. See this link.
Hope this helps.
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