I download my transactions via Quicken's One Step Update, but I verify the transactions by comparing them to the receipts I've collected. I get receipts not just for buying items, but also for withdrawing money from ATMs, depositing checks, etc. I also try to remember when I spend cash so I can enter transactions in my Quicken cash account. For transactions without receipts, I write them down on an index card. This includes returning items. Occasionally, I jot a note on receipt to clarify the category. For instance, I might spend money on postage to return clothes. The transaction will show up in Quicken as USPS, but I want to categorize it as "clothes" not "postage".
The receipts I collect go into a small manila envelope.
Every week, when I download transactions into Quicken, I check the payee name and transaction amount against the receipts in my manila envelope. If the two are reconciled, then I put the reconciled receipts into an expanding file with pockets for different months.
Every now and then, I clean out the expanding file and throw out old receipts. I'm not running a business so there's no need to keep receipts. I suppose if I were really obsessive, I could scan the receipts with a flatbed scanner.