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Short answer: As a Receipt New.
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NOTE: To fully process a customer’s payment there are three steps (New, Allocate and Deposit).
 

New: “New” is always the first required step. Once this is completed, the funds remain on the customer’s account and are posted to ledger accounts unallocated receipts and undeposited funds. 

The check number should be put in the Reference field and the Invoice number this check pays should be put in the Memo field. 

This will allow you to later see this information on the Deposit Report. 
 
Receipt New allows you to allocate a customer’s payment when you record the receipt of the payment. It is, however, not required that you allocate all or any of the Receipt New at this time.  Not allocating the amount at this time will leave the amount "on account".
 
Receipt Allocate can be completed at the same time the Receipt New is entered, OR you have the flexibility to allocate receipts using the icon in the Receipt Group, which allows for a) division of duties, and b) complete deposits before you allocate.