I had the same problem. And I have some links for you that might help.
This is an overview of android build system:
This one is for creating/managing android applications:
This one is for building/running apps:
But I realized that if you are making larger projects, you will want to use all the help IDE and android tools can offer. The intergrated Dalvik Debug Monitor Server is very handy, also intergrated Logcat and all other cool stuff makes developing a breaze. Imagene how many console windows you would have to have opened for one application. Anyways, I still don't like developing for android that much, it feels more like scripting with the java and not actually programming because of all the abstraction from hardware and that kind of stuff.
So I hope those links will help you out.