If your insurance pays you for an auto accident and the insurance company for the driver who hit you do you have to return one check?

If the other company only gave you the deductible amount, then probably not. But if both paid you the full amount, then you should turn the other company's check to yours.  
If the larger check came from the other driver's insurance, I'd return the check from your own insurance company - you're entitled to the deductible amount, if you're not at fault.