Hello there, @lfeinbergdesign

I would also like to organize things, especially in dealing with digital transactions. I wouldn't want my register to look messy when I reconcile them, too. I'll share additional information about connecting your account into QuickBooks.

If the transactions download to one account, connect only the parent account. If the transactions download to the individual accounts, you only connect the subaccounts. Some banks may show the overall bank balance at each subaccount level. This is because the bank provides us with a static balance of the entire account, not the balance of each subaccount.

When it’s time to reconcile your CHASE account, you only need to reconcile the parent account because all transactions in the subaccounts roll up into it.

Also, for your AMEX credit card, as my colleague mentioned above, it will take up to 10 days for transactions to sync with QBO. 

However, if you want to connect each of your individual AMEX credit card and track them separately, you can connect each card one at a time. Or if you want to handle everything in one main account connect to the American Express Credit Card(US) - Parent Account. This parent account automatically downloads all the transactions from your different cards.

Also, for the double transactions, you can exclude it from the transactions downloaded from your bank or financial institution.

Here's how: 

1. Go to Banking.
2. On the Banking page, select the For Review tab.
3. Select the checkboxes of the transactions to exclude.
4. From the Batch actions drop-down, choose Exclude Selected.

Once the transactions are listed on the Excluded tab it will not track or reported as part of your business finances and don't appear in any associated account registers or reports.

For more information, you can refer to these articles:

• About bank or credit card subaccount setup
• Connect your American Express Business account to QuickBooks Online
• Exclude expenses from downloaded bank transactions

After you connect your accounts, you're ready to add and match the downloaded transactions.

Please know you can always leave a comment below if you have any questions about bank transactions. Take care and wishing you the best!