If you have old invoices entered or old payments sitting in undeposited funds, you need to get them cleaned up because your financials are almost certainly incorrect.  This is how QuickBooks is meant to be used for sales/donations:

Option 1:

1. Create Invoice – increases sales and increases accounts receivable
2. Receive Payments – increases undeposited funds and decreases accounts payable
3. Make Deposit/select the payment from the undeposited funds popup window – increases cash, decreases undeposited funds

Option 2:

1. Enter Sales Receipts – increases sales and increases undeposited funds
2. Make Deposit/select the payment from the undeposited funds popup window – increases cash, decreases undeposited funds 

If you have the Nonprofit version you have a special Nonprofit menu which renames “Enter Invoices” to “Enter Pledges” and “Enter Sales Receipts” to “Enter Donations” making it easier to keep track of which one you should use.

Note: If you skip any of these steps, your financials will be incorrect.  If you haven't entered an incoive or sales receipt, you can go directly to make deposit, but iI don't recommend it. 

Also, it’s a good idea to enter unpaid pledges in QB so you can track what’s still owed (using Option 1 above).  You don’t need to send the invoice to your donor.