Hi @Raza Syed ,
You make an Other Charge type item for prepayments. Link it to income, for a Cash basis entity; link it to Liability, if you are allowed to carry liability.
Use this on a Sales Receipt when you get the prepayment.
Use it later on a Credit Memo for the date you are ready to apply it to the actual invoice, to refund it, or to meet Both Needs. Use the icons at the top of the credit memo. Comment back, cheers.