Entering deposits before applying customer payments

I see many instructions on how to 'make deposits' but all refer to entering a customer payment first, to undeposited funds, then the deposit transaction offsets the undeposited funds.  I'm receiving checks for invoices dated last month.  I want to deposit them ASAP, then next week go through them and apply them to the customer accounts.  When I go to make deposits, it wants 'received from' as though I've already applied the payments to the customer.  If I choose undeposited funds in the 'from account' is it going to apply the transaction backwards?  Since I haven't already applied the payments and therefore 'funded' the undeposited accounts account?