Custom CTX format for R12.1.3

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I have a question. We have two templates created for PPR and both use same payment profile option. However we need the File ID Modifier as J for one and K for the other. We dont use sequence. How can I achieve this? I tried to create a separate Profile and attach new XML format to it. However I see Payment Document under Payment attributes is not getting populated and I do know why. Its possibly because new Pay Doc hasnt been associated to Bank account used in template. Can you advise?
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