Gaia and Terra are two different planets, Terra is a much smaller planet and yes there are some hints.


-Major spoilers-



A. The entrance to Terra is the Shimmering Islands, you go down through the islands to reach Terra (meaning Terra is underneath the surface of Gaia.

B. When looking to the sky in Terra you see blue. This is the Gaia's cycle of souls. The entire idea "Till blue turns a scarlet hue" is that when Gaia's blue cycle of souls turns red, Terra has assimilated it.


How storing a planet under another planet is possible is beyond me, if you need some help understanding how they did it ask Garland