In order to create a Vendor 1099 Opening Balance for a 1099-eligible vendor, make sure that the Vendor’s 1099 Type field (Vendor form > General tab) is set to a 1099 type.
Once that is set, the said vendor will be available in the Vendor 1099 Opening Balances form. This can be opened from System menu > Opening Balances > click Vendor 1099 Opening Balance button.
Now that you are on this form, set the 1099 Year and enter an amount in the 1099 Opening Balance field. This amount will also be shown on 1099 related reports.