I don't think they can automatically take payments out UNLESS that is in the contract. I have seen though, banks freeze accounts if there are too many issues with it (overdrawn, extremely late on payments to the point of sending it to collections, etc.) Your best bet is to simply call them and talk to them about it. They want their payments but most of them are willing to work with you.
Another thing...not all the time but a lot of the times, the smaller credit unions are good about working with you on things. When you get things straightened out, that could be something to think about if you are considering switching to a different bank.