It would be helpful to have a duplicate entry or unmatched entry finding feature. My property manager enters items manually when he wants to upload a receipt for an expense. It sometimes takes a day or two for the item to clear the bank or credit card.
To help find matches, a field could be added to the transaction entry screen which would indicate which account the charge will be coming from. For example, purchase made from Home Depot on credit card. When receipt is uploaded, you could indicate to watch for transaction coming via credit card download. Same for when check is written.