Dynamics GP’s Integration Manager is missing the 1099 box. The 1099 Type box is there but not the 1099 check box. Mariano Gomez has a great post on how he solved the problem using SQL. Make sure to check out the comments too for some other solutions.
Importing the Vendor 1099 Box with Integration Manager
Development & IntegrationYear-End & 1099
Archived post from 2009. Dynamics GP and the links it points to have changed since; check current documentation before relying on version-specific steps.