Excellent post Claire! Can't rep you yet but owe you one.
Fedup, as far as books are concerned, I found two very helpful ones.
Amazon.com: The Betterphoto Guide to Digital Photography (Amphoto Guide Series): Jim Miotke: Books
and
Amazon.com: Understanding Exposure: How to Shoot Great Photographs with a Film or Digital Camera (Updated Edition): Bryan Peterson: Books
Jim Miotke also has a blog. Like Claire said, google for specific instances and scenarios. Usually, there's a ton of "how to's" on the net. I do it a lot for PS Elements when I need to.
The manual is really for what your camera can do, all its features and controls so when you find some material on the web to help you get there, you go back to your camera to see "how" your particular camera would get you there. However, it is important to understand the "what" and the "why" as well. DP Review has an excellent Glossary of photography terms. It explains what EC, EV, diopter, focal length, etc. etc. and the effect it has on your photo. I found it really helpful. I think you would too.
For example, articles on the net will explain to you the reflective properties of very bright objects, such as water, sky, snow and sand, and how those would affect your shots if contrast is high. Then you assess your camera with the help of your manual to see how you could adjust for those properties. On top of that, the articles might suggest accessories to help you with the shots, such as filters, hoods, gray cards, etc. For example, people have suggested a polarizing filter. What does it do? How does it affect light and eventually your shot? What is an 18% gray card? What does it do? Do you have to buy it or can you make one, and so forth. So, it isn't enough to read. It really made my hair HURT going back and forth trying to understand and get the concept through my thick NOGGIN. That's when the experts here (obviously that's not ME!
) jump in to help you understand that. Very helpful to their ability to help is EXIF info. It's easier to get to the root of the problem if all info is available to critique.
My advice is to focus on one area at a time. If exposure is your challenge, then read up like a mad dog on it. Start with stationary objects first, so you don't have to fool around with shutter speed just yet. Concentrate on aperture and focus and DOF. When you feel that you are getting the results you want, go to the next, like those that involve speed, and so forth and so on. Biting more than one thing at a time is a recipe for frustration.
We all have gone through the pain of learning a new camera...believe me, I thought mine was broken when I first got it. But reality and then humility quickly set in when I realized it was really all me. But, like my motto, if I think I can and know I can,
you too can.