I've been so confused with Eagle that I was on the brink of giving up, but not anymore. I've just bought this fantastic book which explains everything I need, in simple and logical language.
The first "Eureka Moment" was when I realized what was causing me such problems, to paraphrase the text in the book: Eagle's style of operation seems backwards compared with many Windows programs...
If you are having problems getting started, I can't recommend this highly enough. No connection with the author, just a very happy reader.