Unless the Wageworks card is functionally equivalent to a credit card, I'm pretty sure there is no way to use it on the Web site or app to purchase Amtrak tickets.

EDIT: Just checked the Wageworks Web site, and it appears that the Wageworks commuter card is a stored value Visa/Mastercard. So you should go ahead and enter it into the Amtrak Web site or app as any other credit card, and see if it works.