"Cosa" by itself, to my understanding, doesn't generally mean "what." It mostly means "thing" or "matter" or "affair." There are, however some rather idiomatic phrases that may serve to confuse us into thinking that "cosa" means "what." eg. Cosa stai faccendo (what are you doing) Here the "che" has been missed off but the meaning maintained. I think if you just want to say "what" then the way to go is "che."
I agree with Chris, you can say "Che cosa stai facendo" or "Cosa stai facendo" meaning the same thing, being the latter most used and practical, by getting off the phrase the word "che".
"Che" in phrases like "Che settimana lunga" is to remark an aspect or to make an exclamation about something, while in other instances it isn't really necessary to have "che" like when you make questions as "what are you saying", what are you reading", "what are you eating", etc. (Cosa stai dicendo, cosa stai leggendo, cosa stai mangiando) using just "cosa" in those kind of questions. Hope it helps.