Yes, you can put a clear status to transactions, kmiller2.
Good job for ensuring that whatever transaction you made outside you record it within QuickBooks. In your bank register, there's a column where you can manually set the transaction's status. A blank status will indicate as not reconciled or cleared, C means cleared, and R for reconciled.
I'll show you how:
Here are a few links that will help you in reconciling your transactions:
Feel free to post your questions here. Take care and have a great day!