Ok, have you received the Magma Emblem from the orb guardians at the top of Mt. Pyre yet? If you have, then you need to go to the Jagged Pass at Mt. Chimney. After you jump down a few ledges, the screen will start to shake and an opening will appear in the wall, and that will be where the Magma Hideout is.
After you get Magma Emblem from the old lady in Mt.Pyre, go to the Jagged Pass from the north side, after you jump from some ledges a hole will appear in a wall, go in and that's Team Magma's hideout.
The exact place of the Hideout in Jagged Pass is in the really big rock where the Magma Grunt was standing the first time you went through the Pass. Good luck!
when you go to Mt.pyre you receive the magma emblem after beating team aqua ,then go to the jagged pass and go straight and then the player will say that the rock is responding to the emblem then you can go in there hideout.