For any vendor that gets a 1099, the only method Sages gives for controlling which payments are included or excluded is the GL account. By going to the Maintain menu > Default Information > Vendors > 1099 Settings you can go through each GL account and designate how payments to that account should be handled for 1099s.

If that doesn't work for you there are only two options left.

1-Create two vendor records for each employee so that reimbursements can be made to a non-1099 vendor

2-Manually adjust the 1099 amounts at the end of the year. You can do that by entering a payment (in this case it would be negative) to an account that goes on a 1099 and then also changing the bank account on the payment to the same account.

I'll also add that, while I come down on the side of not including reimbursements on a 1099, there are accountants who argue that a 1099 should include all payments to that vendor because they should be deducting those reimbursable amounts as business expenses.