When you file a Chapter 7, Chapter 13, or any bankruptcy, the protection of the automatic stay kicks in. This is a code sections that causes all collection action to cease. This also causes any companies with notice to cease automatic withdrawals from your accounts.
This means if you have your car and/mortgage payment set up to automatically come out, this will end. You will have to either write them a check, get a money order, go pay in cash, or try to send them some form of electronic payment. Depending on the servicer, some may not take electronic forms of payment. The lenders are not trying to be difficult, they are just making sure they are not running afoul of the law. The consequences to them could be a lot more than the amount of your payment.
Be warned, though, some automatic payments may still occur. The less scrupulous types, like payday loan lenders, may still take money out. While illegal, once they have your money it can be difficult to get it back. If you are concerned, change bank account numbers so no one has access to your account information.
Companies that are independent, and not regular debt collectors, like your gym membership, may still debit from your account. They are not supposed to, but if they are not given notice in your bankruptcy petition, how are they going to know to stop? So if you are cancelling the service, make sure they are included in the bankruptcy filing.
Once you complete the Ch 7 bk or Ch 13 bk filing, then you can resume the automatic payments if you wish.