I've been using AdWords for PPC advertising for a few years, but just recently implemented Google Analytics to our website... The landing pages for AdWords campaigns are tagged with a unique "wherefrom" parameter that is used to collect the info that the visitor arrived to our site through AdWords leading to a conversion -- which is reported in our lead retrieval system. That being said, I haven't turned on the auto tagging for the linked AdWords and GA accounts. Are there any negative effects from doing this? At face value, I can't see that it's having a negative effect, but like I said, I'm new to the GA world and want to make sure we're implementing with best practices in mind. Thanks!
Until you tag your URLs, Google Analytics won't be able to tell the difference between paid and organic search traffic for example. I strongly recommend activating auto tagging in AdWords unless you intend to tag every destination URL manually (which can be a lot of work!).