So long as you have a copy of pokemon emerald, Fire red/Leaf green, and Heart gold/Soul silver (Optional) you can travel to both regions with one character, depending on the region you started with you can access the other either from the Vermillion or Slateport docks. Doing so will transfer all of the pokemon in your party to the PC and cause you to start over from scratch in that region, you will need to travel back to the dockyard of that region in order to receive those pokemon that were moved back to your storage.