Cheque numbering is a challenge if you're using the reference field for anything other than cheque numbers because QBO will always take that number and assume that was your last number, so always be careful with it.

The bank we use generates a file number that shows up in our bank transactions. For example, if my file is going to be 0327, I will number my starting number as EFT0327-001 so that the next one is EFT0327-002 and so on. It makes it a lot easier to match the single line in the bank to the multiple lines in the GL.