"the cake had been baked" is the past perfect tense. The past perfect is constructed with the helper verb "to have" in the past (had) next to the past participle of the main verb.
"I had baked the cake" is past perfect.
"The cake had been baked" is also past perfect, but it is also passive (akin to the difference between "I ate cake" and "the cake was eaten")
this verb tense is used for actions that occur before another point in the past. In the example you gave (#1), the past perfect "had been baked" is appropriate since the baking happened before I left for school.
Sentence #1 is the better sentence.
In Sentence #2, the past perfect is incorrectly applied to the later action. The baking happened first, so of the two past actions, it should take the past perfect.
