downloading credit card and bank txs

When you first start downloading transactions for an existing bank or credit card account, you will almost certainly get duplicate transactions. This is a pain, but you only have to deal with it it once. Go to Edit > Preferences > Downloaded transactions and un-check the Automatically add boxes. This will hold the downloaded transactions where you can delete any duplicates before accepting them. 

Once you have dealt with the initial download, you can download as often as you want and Quicken will attempt to match new downloaded transactions with those already in your register. To match, the dates must be close and the amounts must be the same. You can edit and manually match any matches it misses.

I do not reconcile bank and credit card transactions manually, I have Quicken do it automatically each time I download. This works very reliably. The only downside is that if I have written a paper check and the recipient does not cash it, there is no obvious notification other than scanning through the register and looking for missing R's.

After setting up an account for downloading, you can select the Auto reconcile option on the account's Reconcile screen.

One other note on credit cards, if you are not doing it already, is when you have an account for the credit card, you should assign Categories to the transactions and enter the monthly payment as a transfer from your bank account to the credit card account, not as a payment with a complicated split. That is a big time saver.

And always make lots of backups.  Like backup before downloading so if something goes wrong or you don't like the results you can go back.