Hi Trinath,
In your entry above, the FI transactions are residing in two different GL accounts even though you are using the same Employee Vendor number. One is the regular vendor account (Normal items of FBL1N) and the other is on the Special G/L. I doubt clearing these automatically through F.13.
The standard process is to adjust the invoice with advance through F-44 immediately after Vendor invoice posting. There is a risk of making duplicate payment to the employee vendor if you do not adjust this advance in time.
Please review the process and let us know if the above answers your query.
Thanks,
Basavaraj