To only pay one of the vouchers through the AP Check Process all other vouchers need to be put on hold.  To put the voucher(s) on hold follow the steps below:

• In Purchasing > Actions > Voucher, change Mode=Hold
• Click the All checkbox to select all vouchers
• Uncheck the S checkbox for the 1 voucher that needs to be paid
• Choose Action > Hold
• Run Pre-Check Writing Report to ensure only that 1 voucher is listed
• Run the AP Check Process as usually done to pay the voucher 

After the check has been printed the vouchers can be released from the held status.  To release the held voucher(s) follow these steps:

• In Purchasing > Actions > Voucher, change Mode=Release
• Click the All checkbox to select all vouchers to be released
• Uncheck the S checkbox for any voucher that needs to keep the held status
• Choose Action > Release