Hi charliandlenni
Have you already created Spend Money/bill transactions from the InTray documents? If so, the bank transactions should be matched to these already created transactions, instead of being allocated to accounts. Allocating bank transactions to accounts will create new Spend Money/Receive Money transactions, which effectively will be a double up to transactions created from InTray documents. In this case I'd suggest undo the bank feeds allocations, and match them to the Spend Money transactions/open bills already created in MYOB Business.
If the InTray documents haven't been used yet, you can consider linking them to the Spend Money transactions created from the bank transactions instead - Working with InTray documents.