Let's take an example, you have created an invoice INV34 for 100 rs
and customer has given you 150 rs.
You have to create Receipt From Customer (RCV23) > Receipt Against Invoice
Select 100 rs against INV34
and rest 50 rs in Advance Payment
Next time, you create INV54 for this customer for say 72 rs
So, you will edit the old Receipt RCV23 > Receipt Against Invoice
and you have to type 50 rs against INV54 and delete 50 rs from Advance Payment
Because now it is being adjust.
Save the receipt voucher.
It will now show 72-50=22 rs pending against invoice INV54.
For these 22 rs, you can make separate Receipt voucher.