Multiple Payment Sources

I’ve written a plugin with a new payment gateway that gives customers an “allowance”. This part is working as expected. If, however, they use up almost all their allowance but would still like to make a purchase I’d like to remove their remaining allowance balance from the total and then allow them to finish with another payment gateway. Any suggestions on how to pull this off?

I’ve tried modifying the total within the WC_Order during the payment process as well as modifying the WC_Cart and had no luck. Any suggestions?