This is why bank preventing unauthorized withdrawals is so useful. And credit card processor disputes too.
I'm not an expert on this, but I believe there are ways to set up business accounts where money can't be taken out in that way, at least not by the standard electronic means. You can also manage accounts in such a way as that there's no money to take out, although that does not necessarily prevent the account from going into the negative. Checking accounts can go into significant negative balances if the bank chooses to allow it.
As to prevent the overdraft, just ask the bank to NOT have overdraft capacity on your account(s).