In order to apply manual payment to clients invoice one need to perform below mentioned steps:
1) Login into Modern Bill admin area.
2) Search the client order.
3) Click on pending invoice number from account register list.
4) Click on Apply Payment link from bottom.
5) Search the invoice number from search invoice box with selection of pay option radio button.
6) Enter Amount in Amount Paid box.
7) Enter Transaction ID or Comment which one need to display in account register description section.
8) Click on submit.