About command-line tools... you're going to learn them anyway, so why not at the beginning? You're bound to have to get your hands dirty yourself with an IDE anyway when the automated build process is not exactly what you want...
Granted, I don't personally know how to really use autoconf/automake, but I'm trying to get there eventually... start with plain make, or with small excercises, run the compiler by hand. It's not that difficult, and as you work your way up from the bottom, you gain an understanding of what goes on behind the scenes when you press that shiny "build" button in your IDE. Most importantly, when that button fails with esoteric build errors, you are not totally stuck.