What you have to understand is that Banks have accounts at the central bank and they can just like you and me keep money on those accounts, overdraw etc. That's actually how the central banks get money into the system: they create the, from thin air and just transfer them to the Banks' accounts. Negative rates work by punishing banks if they don't withdraw enough money from those accounts and get them into circulation. So if a Bank had money on that account that money would start getting less. That's what they called Negative rates. It's a bad name. When rates are positive the bank has to pay back the central bank with interest namely the famous "interest rate" that's for the US Fed at 0% to 0.25% so lol.

Source: I used to work at a bank. Nothing to do with money mind. Software dev. That stuff was part of the apprenticeship course.

I might be wrong though so CC @President_Satan to check or add anything.