Negative Check Amount in AP Payment Group

We run into an issue with our largest supplier where it's difficult to take credit memos when running AP checks. When Epicor brings the invoices into the group it sorts the payments from highest dollar to lowest dollar amount. Because of this our last check will have a number of low dollar invoices and all the credits causing a negative check, which gets kicked out. Is anyone else seeing this and does anyone have a good solution? My current solution is create a separate group and manually select the invoices to pay collecting the credits and a few high dollar invoices.