It depends on what type of account it can draw from and if you have that account already set up.
Lacking any extra detail, let me assume this is a card attached to business checking and you can use it as if it were a VISA or with the PIN direct withdrawal from checking at point of sale - or even to get cash out of an ATM.
Unless you want to track separately these transactions, there is really nothing you need to do other than code the reference number in check/expense to indicate it was not a paper check.
You can set up sub accounts of checking to track separately the debit transactions separate from ACH but I do not see the point as however you use the card it draws directly from your current bank account
