Auto is Auto I'm afraid. You are only in charge of where you point the camera. To do what you want, turn off auto but set the ISO to auto (menu option), aperture to auto (on the lens), set shutter speed to auto (Top of camera). Then either select manual focus or A+M (menu option). If you have A+M active, it focuses automatically, but if you keep the shutter half pressed you can manually tweak the focus on the lens focusing ring.
One last tip, if you are in Manual focus mode, but find your subject is massively out of focus and you don't want to spend all day spinning the focus ring, you can press the AFL button and it will auto focus. Do this to get focus "in the ballpark" then continue to tweak as you require manually.
Hope this helps... have fun playing with you camera!
The Auto switch puts the camera into a full-on idiot-proof "point-and-shoot" mode. Many options are disabled or overridden in order to prevent mistakes.
The main use for Auto mode is when you hand the camera to someone else, such as to take a picture of you. Instead of having to undo all of your custom configurations, then having to redo them when you get the camera back, you just switch to Auto, hand them the camera, and switch back from Auto when you get the camera back.
About the only time a knowledgeable photographer is likely to use Auto mode for themselves is when an unexpected photo opportunity suddenly pops up, and you don't have time to reconfigure your camera. You can switch to Auto in an instant and try to grab the shot. You'll have to deal with the output being just Provia JPEG (no Raw, no other film simulations, etc.), but it does generally do a pretty good job of at least capturing the scene.
