Hi Haritha,
I don't understand what do you mean by 'vendor master also maintained in SGD and USD'. The thumb rule is SAP won't clear documents with different currency, meaning if you have a credit memo posted in SGD currency it would only be adjusted with an invoice posted in SGD currency else payment run won't pick that document. You may create a test case and try this. Post an invoice for 1000 SGD and you would see the credit memo would be adjusted,
Thanks,
Sajin