Can you put auto loan in checking account?

Assuming I've understood the question properly, no you cannot. You don't get handed a big pile of cash to do whatever you want with when you get an auto loan. You get a piece of paper saying that you've been approved. When you pick out a car, the dealership gets the money directly from the bank and sends them back the title. You never have the money, so you can't "put it in a checking account."

Now, there's a possibility that you're talking about a secured loan, in which you're putting the title of a car (or some other asset) that you already own up as collateral for a loan. In that case you DO get cash (well, probably you actually get a cashier's check) and you can do whatever you want to with it... you can pay your mortgage, buy a new TV, put it in your checking account, or just get naked and roll around in it; the finance company doesn't really care, because paying it back is your problem and if you don't do it they'll take your car.