Question about Bleach and when Aizen took charge of Hueco Mundo?

I am a little confused... When did Aizen take charge of the Espada and Hueco Mundo?? Because I thought it was right after he took the Hokyoku.. But after watching the Arrancar Arc and the Flashback about Neliel and seeing that the roof was colored to look like the sky (and it was said Aizen did this).. Does that mean Aizen was in charge of Hueco Mundo way before he took the Hokyoku? Cuz it is said that it had been a really long time since Neliel had been the #3 Espada and defeated by Nnoitira.. or is this just a minor glitch in the story time line?? Any Idea's