I'm here to help, @MDBR.
In your case, you'll have to reconcile first before creating a journal entry. If you do it the other way around, this will confuse the reconciliation process and will show duplicates.
When posting moving forward, you'll need to ensure these are allocated to the correct accounts so you can reconcile all the transactions easily.
Should you need other references for banking transactions, feel free to visit our site: Banking and Bank Feeds for QuickBooks Online.
Please let me know if you have further questions about your sub-accounts. I'll be more than happy to help out.
