Hi there Blandon! I would say that moving out of "auto" mode is a step by step process. I would suggest moving into AV mode, or TV mode before going on full auto. Then maybe playing around with the metering mode. Looking at the exposure data, while you look at the photo, will clear a lot of things up for you.
I doubt I will ever try to manually focus a camera again. My eyes are shot - way slower than a good lens! I still have my old manual Nikon, which takes great shots. I just can't focus the darn thing. I love autofocus!