My mother browwed 2,000.00 from her boss to pay her car. He stopped payment on the car payment and he has my check so what can I protect myself with stopping payment on the check

I don't understand the situation totally. Did you pay your mom's boss some money to pay for money your mother borrowed from her boss? Then he is not making payments on the car for some reason? Or did he stop payment on the check that your mother borrowed from him?

Sounds like there is some confusion in this situation. Is it possible to talk with her boss to find out why he is stopping a payment?

Your mom borrowed money from her boss to pay for a car.

Who owns the car
Was the money a loan, a advance in pay
Was the loan written
Why did he stop payment on the check

Then, why did you give him a check for.
Was you paying him back for your mom
If so why did you not just give her the money