Designing Great Beers by Ray Daniels is still a great book to get you started in designing your own recipes. Sure there are more malts and hops available nowadays, but it will get you headed in the right direction. Use software to get your numbers in the right place, but use the book to help select the right ingredients for the styles.
I agree. I hadn't realized how old that book is, though, until I picked it up recently to refresh myself on a couple of styles. Regardless, what I think is great about it is the way he provides the commonalities and differences between a variety of beers of the same style.
When I first started designing my own recipes I used a similar approach of taking three or four recipes from quality sources (mostly BYO at that time) and looking at the similarities. Which base grain is appropriate, which hops, etc. Then, tweak it over time to get what you want.
Major's advice is solid, but I also think you need a guide - especially when you're starting out - to help you determine which base malt or hops or clean ale yeast you want to use in the American Pale Ale. Particularly if you want to stay on style.
Of course, I've also done a bunch of crazy beers where I've just throw together whatever I had and they came out pretty good, too.