Dear Soumya,
Withholding tax would calculated at the time of Invoice or at the time of Payment whichever happens first. So you need to maintain the WT types of payments also. Posting key 39 is used for special gl transactions. As you said that you are not calculating the WT at the time of payments then discuss this with your client how they want to calculate for special gl transactions. Hope this is helpfull. Thanks.
Regards,
Ahemmed