ACH and/or EFT via web service

I'm not holding out much hope given what I've read in the documentation and online help (assuming I'm understanding correctly), but here is the scenario I'm dealing with.

We take orders from individuals who pay for our services directly, however their Sales Orders are attached to one of several customers. For example, the fictional customer University of Schwa has a nursing program which requires candidates to provide the results of a criminal background check to ensure they can even be licensed in their state before paying for 4 years of school only to find out their criminal record precludes them from working as a nurse. The prospective students pay for the background check out of their own pockets, but the Sales Order is attached to the University of