APP problem- setting off debit and credit items of a particular account

Hi,
We have configured APP for vendors. Vendor is having 2 line items as open:
Invoice- Rs 10000
Down payment (posted thru special GL) - Rs 3000
System always pays the invoice amount of Rs 10000/-. Could someone please tell me how can we make a payment to the vendor after netting off the down payment of Rs 3000/- ? I want APP to pay only Rs 7000/-. Debit balance check only works if the vendor account is having -ve balance. Please clarify.
Regards
Suresh

Hi Raj,
I will tell you my situation:
1. Vendor invoice is pending with an amount of Rs 10K
2. I have an amount of Rs 2K as advance paid to Vendor through Special GL (posted not using f-47 and f-48, but only through F-02 using special GL "A")
3. I have enabled special GL transaction "A"  also in the APP configuration for vendors
4. I have assigned the incoming payment method "E" in the Vendor master record
5. I have maintained the incoming payment method in the line item of advance payment
6. While executing APP, i mentioned payment method "E" also in the selection parameters.
Even after doing all these, APP is not netting off the amount of Rs 2 K against 10K
Please clarify if i am missing anything.
Regards
Suresh

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