I wouldn't worry about the cup thing for water/ bottle for milk. you will more likely do more harm offering the bottle than you will simply offering her a cup for beverages.
She won't be confused...both my girls only ever had water for BM or milk at that age, all from a cup. It is at the stage now where DD2 can differeniate and tell me if she wants boob or water - if she wants a feed or is simply thirsty. It has actually helped immeasurably. She has milk occasionally (rice milk) in cups also and has never knocked back water for milk or vice versa.