The trick here is the word that comes after in, alto. In means in, but in alto means above, in the upper area!
Su is generally used with movement (Voglio andare su - I want to go up) and for translating "on", as in on the table, sul tavolo, on the wall, sul muro.
In alto is generally used to point at a general location. Sono in alto. I am above.
Hope this helps!