Hi, Cy.
When Quicken downloads new transactions for your checking account, it lists the new ones in a separate window below the area where you manually enter transactions. Then it compares the dates and amounts with entries that you've already entered. If it finds an entry that appears to be "a Match", it flags it in the Registry and presents a small menu that includes the option to "Match" the manually entered transaction with the downloaded one. If you accept this option, the Clr column changes to a "c". (The "c" will change to "R" when you Reconcile the account.)
No, it doesn't make a duplicate entry in your Register - but if it doesn't find a Match, then the new entry will be labeled "New" and you will be offered the choice to Accept it as an entry. If you are reasonably careful in entering transactions as they occur (on the same day you write the check, for example), you should seldom see a "New" entry, except for direct deposit of your Social Security check. ;