This happens often when I place an online order and am charged or each item separately when they ship.  The low tech method I use is to simply make multiple copies of the receipt, one for each CC transaction.  Then I change the total on each receipt to match each transaction, and then pair them up.  Its ridiculous but it seems to work until the QBO team get their act together. 

I am frustrated that I cant simply add multiple bank transactions to one receipt.