ok so i am leveling Aqua up in the Final Episode so dose that mean when i go and play as Aqua in her story she will be the same level and have all the Mirage Arena things cleared or do i have to do it again in Aquas story?

final ep. and aqua files are separate. if u want them to be the same lvl then play aquas and when u r ready to take on final ep. just beat aquas story everytime u do it will ask if u want to save final ep. data then ur new stats will be loaded to a final ep. file.

oh ok lol that makes seance guess i should be leveling her up in her file insted of final ep.

No. So for example let's say you are level 39 with Aqua in Final Episode. In your Aqua save file, you'll be at a lower level then what you leveled up in Final Episode