Hi Suhas,
When a particular payment lot item hits the payment CWL, then the value for the CWL GL A/c comes from the posting area 1040.
Now if you are performing a Cross Company Code posting from the payment CWL for that item, then you have maintain posting area 0030.
Apart from that I don't think there is any change in the clarification GL A/c when you process it from payment CWL.
Thanks,
Amlan