Who kidnaps Amanda on the season 2 finale?
Latnok kidnaps both kyle and amanda based on spoilers for the season 3 premiere. kyle awakens in a latnok building restrained and weakened and he must escape and rescue Amanda.
What song was played in a certain scene/episode?
You can find a complete list of songs, including scene descriptions where they played, here: http://tvshowmusic.com/shows/kyle-xy-music-season-3