If you need only part of a Voucher amount included on the 1099 Report:
  1. Check the 1099 box on the Voucher
  2. Go to the Vendor supertab and find the Vendor
  3. In the 1099 Adjustment box enter a negative amount equal to the amount of the voucher that should not be considered
  4. Optionally, you could leave the 1099 box unchecked on the Voucher and simply add the amount needed for the 1099 Report into the 1099 Adjustment box
The more appropriate way to handle this would be to create the voucher with multiple line items.  Separate the voucher into 1099 and non 1099 amounts.  Then tag the voucher as a 1099 voucher and on the line item tab, select the correct box for the line that should go on the 1099 and leave the other line as "none".  This will bring only the 1099 line amount into the 1099 calculation.

If the voucher wasn't split during data entry, then the use of the 1099 adjustment box is required.