I use a different numbering system for the EFT payments.  With QB desktop I had to number the EFT payments manually.  But with QB online, I found that you can type the starting EFT number in the payments window and then it will automatically increment each one.  But, you have to do the EFT and cheques in separate batches of course. 

One big problem, though, is that you can't print the remittance slips in a batch.  For some insane reason, you have to open each payment as if you are going to edit it and then print from there.  Then, close it and open the next one.  Why Intuit?  Why?