This is done in Accounts Payable --> Main Menu --> Manual Check Entry.  For a Check number, choose APP then add a sequence number, such as APP001.  Enter the vendor and date.  On the detail lines tab, select the two invoices.  It will apply one to the other and leave the remaining as a credit balance. Print, Review and Update.  Check Vendor Maintenance to confirm. 

Hello Stefanoum, thank you for your answer the issue that I have is that when I accept the transaction is telling me that the manual check and payment entry is out balance. 

Manually type in the correct amount for the first line.

Thank you Kevin! it works. 

Hi Carina Cavallini, if this suggested answer helped, please mark it as verified  (by clicking the "Verify Answer" button next to Reply, on the response) for the benefit of others in this forum . Thank you!