@AileneA  re: In QuickBooks Desktop, when paying a 1099, you typically enter the payment method in the "Payment Method" field. 

"When paying a 1099"? That doesn't make any sense. 1099's are filed, not paid.

What are the keywords to enter in the doc number field on a check so they're excluded from the 1099 Misc?  I think VISA is one, and perhaps EFT?  PayPal?