Ender's Aiúa at first lived solely within himself, and after going Outside it resided within him, Valentine II, and Peter II. After Ender lost the will to live his Aiúa left Valentine and his original body and then was solely in Peter II. Ender communicated with the Hive Queen through philotes but his Aiúa was never in her.
The Ender’s Game book is the oldest entry in the series and thus is riddled with inaccuracies. The age given in that book is no longer considered canon by the guidelines of the wiki as newer content contradicts it.