I entered two purchase invoice in manager without any invoice number and also i made payments in advance but after that i updated my invoice with numbers and also assign payments against specific invoice but it is still deducting from previous balance rather than that particular invoice. Please tell why it is doing us even though i have updated my transactions
Your explanation is too vague to understand exactly what you did. Be sure you have read the Guides:
If you still have question, be more specific, and post screen shots of the transactions.