you are right that you used journal batch name and the number series functionality. in addition, it also allows to skip some document number, but i think it is somewhat tedious since you have to go to the number series everytime you want to skip a certain series by inputting/editing the last number used, where you need to enter the number prior to the number you intend to use.
would the option of using the external document number for the cheque number be feasible and possible on your business process?