Is there a way to have overflows print at the end of a check run when using the same printer for both overflows and checks?

Mekorma overflow reports get inserted into the check run and do not print after all checks.

To prevent interspersed overflows in the check tray be sure to use a multi-tray printer. 

If the client prefers to print the GP Separate Remittance report with Mekorma checks, the Separate Remittance report will print at the end after checks print but the stub portion of Mekorma reports will not report the full page of line items, a known issue of mixing Mekorma with GP Report Writer for Separate Remittances.

Workarounds with a one-tray printer:
Use the Mekorma overflow format and designate a pdf printer for the overflow reports.

To print separate remittances using the Dynamics GP Report Writer, check the 'Use Pre-Printed Check Stock' option on the Mekorma MICR Setup (Payables) screen. When you check this option, the option 'Use Check Format (First page) for overflow pages' field changes to 'Print separate remittance for overflows'. Check this option to print separate remittances using the Dynamics GP Report Writer. If checked, the Overflow Page Format field is automatically disabled and separate remittances are set in place of overflows.

The use ‘pre-printed check stock’ option in the Mekorma checkbook setup window stops the batch from ordering checks based on the payment amount (by threshold). Therefore we recommend against marking to ‘sort by threshold’ (in Mekorma Security Setup) with the use of the ‘pre-printed check stock’ option.

Mekorma Recommended printers:
https://portal.mekorma.com/articles/details/Article/KA-01076/what-printer-should-i-use-to-print-checks-in