Direct deposits and payments are usually passed through your bank to whatever clearing system applies. They have a good deal in common with cheques/checks - and will incur similar fees if there's no funds left to make the payments
The actual protocol will be the one your bank has set up for its customers, and they will then package up the transactions and add them to whatever processing stream they pass to the settlement agency. Banks usually accept common electronic means of transmission - dial-up, floppy disk, mag tape ...
But you can't interface directly with the clearing system, and have to go through the banks. Good news is its pretty common, and the bank should have good information and a range of acceptable ways of getting the data to them. Bad news is that it may change if you change banks.
Contact the bank and ask for their elctronic banking experts.
