You can add more amount as advance payment against a sale order. For this 

1. Go to the Account Voucher Main - F T V
2. Select Receipt Voucher - F6
3. Select the ledger in To "Advance Against Order"
4. Enter desired Amount (Credit Side)
5. Select Against Reference as Type in Bill-wise Adjustment Screen
6. Select Reference (for example AdvSO/1286.0001, You can find this number printed on the sale order)
7. Save the entry and this amount will be added in that order.

Related Question

Faq : What if my customer has not brought the sale order receipt and want to make more payment against existing order?

Ans : You need to open Sale Order Register and find the reference number against that sale order. Now use the same number to do the receipt entry.