I had customer use a new AMEX card to make a payment and the payment shows processed and deposited,, however the deposit is not in my bank and they show no sign of it.

Hello there,

Even though the payment shows as processed in your AMEX bank, QBO will take additional time to process the transaction. Let me provide you more information about this.

The time it takes for deposits to appear in your account varies based on the product you are using and the type of payment involved. Standard deposits are processed every day except Sundays, Thanksgiving Day, and Christmas Day. Alternatively, Instant Deposits are available year-round without any exceptions.

If you're new to QuickBooks Payments, we'll deposit your first set of payments within 5 business days. These early deposits take a bit longer while we set up your account. Once we set up everything, we'll deposit customer payments much faster.

For more details, feel free to check out this article: Find out when QuickBooks Payments deposits customer payments.
 

Moreover, after you can also consider categorizing your transactions ensure they belong to the right accounts.

Let me know if you need help with your received payments or have other concerns with QBO. We're always ready to help.