I've seen Season one 5 times!!

Jimmy and Pussy were mixed up by corrupt cop, Vic Makazian. Tony desperately wanted Jimmy to be the rat and not Pussy, as Tony and Pussy were best friends. As for the hotel secene and Silvio saying, "You should call for help down your microphone", Jimmy said, "Oh god" when Silvio put the gun to his head. This isn't a reference to being a rat, this is Jimmys way of saying, "I'm a goner". Jimmy knew that his "friends" had thought that he was a rat and Jimmy went for his gun because he thought that he might have had a chance to kill either Chrissy or Silvio, or both.

After Jimmy was found in the alley, Skip said to Pussy, "Jimmy Altieri ate a bullet for you". This mean't that Jimmy wasn't a rat.