After getting the Magma Emblem and defeating both Team Aqua and Magma, you must go to Sootopolis City. Then go to Sky Pillar, near Pacificlog Town(Rt. 31), and awaken Rayquaza. Then go to Sootopolis again, and there you have it!
This videos should help with whatever problem you have
And if this doesnt help have you gone to the top of sky tower(i think thats what its called) to get raquaza to come down and stop kyorge and groundon from fighting because thats something you MUST do to get into the gym. If you can find the tower on you map its on that route in between defowg(location of the second gym) and saltport(location of the boat house and museum). Have you also battle team magma in the underwater cave to make them awaken groudon and same for team aqua.