I haven't tried it with ACH, but I know it can be done by wire transfer (not ACH, but good old fashioned SWIFT). You can pay more than your balance, and you will see your "available credit" increase.

I would expect it can be done by ACH if you initiate the transfer from you bank's side. (Probably you cannot initiate it from the Chase site because chase would not allow you to create a payment for more than your balance.) But because I have not tried it, I cannot give any guarantee.

Some card issuers, such as BoA/FIA don't allow this at all, which is quite dumb.