Your organisation should be decentralised, comprised of small isolated cells, and, if anonymity is possible, rely on hired hands a lot.
The chain of command is necessary, but it should be set up in such a way as to prevent the vampire from going up the chain. For example, each level should never communicate directly with the other. Depending on your tech level it can be letters, emails, or some other signal system that allows for complete anonymity. If you want maximum security, you have to use disposable recruiters at the early stages and you might need to kill cell members if one of them gets promoted to the higher level.
Break each level into small independent cells that do not communicate with each other and have no way to identify each other. If one of the cell members is captured by the vampire, only their cell is compromised while the organisation itself stays safe. Give cells a lot of freedom so your organisation does not create patterns of behaviour that a vampire can track.
If your world allows anonymity to employers, use as many hired hands for small inconspicuous tasks as you can. Again, make sure that you do not create any noticeable patterns. Do not deliver all your mail to the same address.
Also, make sure that your organisation has some talented bookkeepers. Money flow is the easiest way to track big organisations no matter how secret they are. If you want to succeed you need to hide your money really well.