If you only want to get Quests to complete, then you can do that "in-game" using the Console.
There are a number of commands, depending on how you want to do it.
You start the Console by using the
` key
Start here: http://www.creationkit.com/CompleteQuest or here: http://www.creationkit.com/SetStage
There are other options you might find better for you: http://www.creationkit.com/Console_Commands (it's a big and not always well-named list!)
You could actually amend the quests in the CK ... but, if you have saved the game you want to see the changes reflected in ... You're probably out of luck as the original quest-variables will probably persist in the saved game itself.