In the manga she worked for Ganondorf, which is fine for the story but really makes no sense for the game. My best guess, and this is a guess I need to study it some more, is that she spent her time simply preparing for the hero's return. As soon as Link awakens she is waiting for him, and tells him what he needs to do next. The only way she could have obtained this information is by closely monitoring the situation around Hyrule. Truth be told, she probably did more exploring than Link. She somehow managed to discover all of the different warp point songs to teach him upon his return. This may have come in handy with her survival as well. If the power is in the songs and not the ocarina of time, she could have used them to teleport to different locations whenever she was close to being caught.