Is there a way to mark items as clearing the bank before it is time to reconcile? Without marking with an "R"...so it doesn't mess me up later when I do reconcile.
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:
Go to the Accounting menu and select Chart of Accounts.
Look for the account where the transaction was posted. Click View register.
Locate and select the transaction.
Under the Reconcile status column indicated with a checkmark, repeatedly click the box until you get the C status.
Here are a few links that will help you in reconciling your transactions: