When a client pays before you've invoiced the work, open the client and use Advances → Record advance: the date, amount, how they paid and a reference. Each advance gets a number (RV-00001 and so on).
India: GST on an advance for services is due when you receive it. Choose the GST rate when you record it, and MSMEPulse works out the tax inside the amount for your receipt voucher. Choose 0% for goods. Check how to report it in GSTR-1 and GSTR-3B with your accountant.
Apply it to an invoice
When you invoice the work, click Apply next to the advance, choose the client's unpaid invoice and the amount. It's recorded on the invoice as a payment, and what's left of the advance stays for the next invoice. An advance can only be applied to an invoice in the same currency.
The client's statement shows the advance once, when it was received. An advance that's been applied can't be deleted.