Hi Anusha
You can probably make the following process changes and enhance your existing process:
1. The salary information is being sent as a GL Upload information. In such a case, you can ask the pay roll company to send this information employee wise. Once this file is interfaced to ECC, it should create an invoice on employee vendor
2. On the positive pay part, i am sure this information is sent employee wise with check information. So you should write an enhancement which will create a payment document as well as check in the system for the payment document, once the positive pay file is interfaced to ECC.
This enhancement should take care of your EBS posting as well automating the same.
Thanks & Regards
Sanil Bhandari