Let's see, there must be a topic on this on the support page...http://www.youneedabudget.com/support/article/how-to-reconcile
"Reconciliation is the process of making sure your YNAB account registers match your bank accounts, and resolving any differences between the two." Basically, even though you've imported your transactions, reconciling them locks them to keep you from changing them without getting a warning.
Because of this, there's no need to mark things cleared in your register. Some people want to do this to indicate that their manually entered transactions have already been matched to transactions in the bank's records, but it's not necessary, because the reconcile function pulls all unreconciled transactions within a time period, whether they're marked cleared or not.
If you import, BTW, you should do so frequently. That way your category balances will be accurate. Of course you'll check the balances after they've been added to the register, so you can spend by those category balances instead of bank balances.
"It’s still all about the method. Fancy Cloud Sync algorithm aside...the software is there to help you become more aware (Rule One), anticipatory (Rule Two), flexible (Rule Three), and secure."--Jesse's blog, A Method to Your Madness