Usually "essere" (io sono) is used for identity, qualities, permanent attributes, etc. while "stare" (io sto) is for locations, in the continuous tense and in idiomatic expressions like "how do you do" (come stai) but don't take it as a rule - there are a lot of other uses and exceptions.
I can't say this for sure, but knowing what I know of Spanish I'm assuming io sono=I am in the sense of something definite. Example: I am Samantha=Sono Samantha. For io sto=something indefinite like emotion/how ones feeling at that particular moment, etc. Ex: I am well= sto bene.
"How do you do" is a very strange phenomenon in English. You use it only when you meet someone for the first time - ever. (After that you use: "How are you?" etc.) But this is all very, very formal. Just don't use it to ask how someone is. Trivia of languages are so strange, no?