Notes are written above the same rhythm notation. Every note out of any scale has a symbol. In a song in the basic scale, which in western notation would be the I, II, II, #IV, V, VI, vii, I, the song starts with a symbol telling you the scale, and the notes are thought of as numbers- from so to sesa. The symbols are:
If you choose a different scale to start with, you would number them the same with the same symbols. If you switch scales, you would notate that in the music and continue.