"Prego lei" doesn't exist. The answer is "prego" or "grazie a Lei/a te" if you also want to thank the other person.
"Prego a tutti i santi" is not correct: prego tutti i santi, without "a".
When a waiter says "prego" he's saying "go ahead and have a sit", "go ahead and tell me what you'd like to have". It means that you are welcome there and that you'll be treated right. At the post office the employe will ask you "prego?" - tell me why you're here. And so on.
If anyboy here speaks Russian, it's about the same as "pozhalujsta".