In a post published on 29 April 2013, Google announced that
Starting in mid June, you’ll be able to import your Google Analytics goals into AdWords shortly after they’re configured. As usual, data for those goals will be available about two days later.
Google suggests that it’s better to track Goals through Analytics rather than AdWords for the following reasons:
Google Analytics Conversion Goals
AdWords Conversion Tracking
GA Goals will still be uniquely manageable from GA Admin. There can be discrepancies between the two, as Google explains here together with everything needed to let GA goals appear under your AdWords campaigns conversions list.
You can use both, they will not interfere each other so no need to change configuration.