Hi babylocks. Apple has a wealth of support document's that will help you in updating your iPhone 3GS to iOS 6.

You should first back up your content with iTunes. You can find information on how to do that here: iOS: How to back up and restore your content

There are instructions on how to update your iPhone here: iOS: How to update your iPhone, iPad, or iPod touch. Scroll down to "Additional Information" and you'll see "When updating from iOS 4.3.x or earlier, see iOS 4: Updating your device to iOS 5 or later". Click that link for the additional information.

I want to stress to you the need to back up your iPhone content with iTunes before you start the update process.

Good luck!