If the credit memo pays the invoice off completely: 
Configure Business Rules to show all invoices and credit memo applications on checks:
  1. In Configuration, click Business Rules
  2. Highlight Invoice
  3. Unmark the Change invoice status to paid when applied credit reduces the balance to zero checkbox

Note: With these settings, a zero dollar check must be printed for invoices fully paid by a credit memo to change the status to paid. This change is not retroactive.

Configure the bank to print Credit memo applications:
Per check run: 
  1. In Banks, click Print Checks and Record Bank Drafts
  2. Select the Format tab
  3. Click Edit Payment Options
  4. Highlight Check Stub Information and mark the Include credit memo application checkbox
  5. Click OK

Per Bank's setting for all check runs:
  1. In Banks, click Edit account details
  2. Click on the Payments Tab
  3. Highlight Accounts Payable Computer checks
  4. Click Edit Payment Options
  5.  Highlight Check Stub Information and mark the Include credit memo application checkbox
  5. Click OK