Tile Layer Pro?

Do you mean ingame? Tile layer pro (like YYCHR or peerspriteviewer) doesn't import the palettes to the game. You can load/save them, yes, but only for reference, for making you easier to edit sprites. What are you trying to import? Characters? You could use FF3usSpriteEd or even ff3usme for that, and those programs change the palettes...