If your bank statement shows a lump sum for each deposit, group your payments for later deposit. If your statement shows each individual check you deposited, you should deposit the payment directly in a bank account. It's easier to reconcile your QuickBooks accounts with your bank statements when the accounts show deposits the same way that your statements do.
QuickBooks “holds” all your customer payments in a special account named Undeposited Funds. To move the payments to your bank account, use the Make Deposits window to group the payments into one deposit. This method works best when you hold the money you've collected for a period of time before you deposit it, or receive several payments that you deposit together in a lump sum.
QuickBooks deposits the payment in the bank account of your choice when you record the payment. The payment does not go into the Undeposited Funds account, and you do not have to use the Make Deposits window to deposit the payment.