FPY1 payment run

Hello Experts,

We have on scenarios like that

1) We are running payment run with daily scheduled jobs.

2) this payment ( FPY1 ) run with only CC = ABC, so that all the BP/CA selected for this run

3) There are 2 BPs and 2 CA associated with them

4) There is no payment method assign in CA,actually we give payment method at document Level ( FPE1 )

5) BP1-CA1-D1 ( have payment method D biller direct incoming )

6) BP2-CA2-D2 ( have payment method E Direct debit payment )

7) While job runs it is taking only payment method E,hence document D2 is cleared,but D1 is selected but not cleared.

8) So my doubt is how we can change the job or associated program so that it fills payment method D as well.

9) Or is there any table from where the payment run program picks the payment method.

Please give some solution for that.

Thanks & Regards

Amit