I'm grateful to welcome you here in the Community forum, sgray. My top priority is to give you the clarifications you need in the Community.
Let me help you clear things out by answering your questions individually.
First, outstanding checks don't have a C or R status in the Bank register. This is how the system knows them. Second, you need to match the downloaded checks to the manually entered ones, so they are not duplicated. Lastly, you skip the uncleared checks when you reconcile.
You can also add new accounts if you ever need to keep track of other types of transactions.
You're always welcome to drop by again if you need further clarification about outstanding checks or any QuickBooks-related concerns. We're always here to assist you. Have a successful year!
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