There are three colour palettes namely - original, harsh and gray. So can I use all six colours or just two colours per colour palette meaning I get to use only two colours. ?
Welcome! You can only pick one of the palettes. Your game can only be two colors. If you would like you can include a palette swapper as a game setting.
It can't be an actual mechanic of the game. You could allow a player to swap palettes with a keybind in game if you want or it has to be in a setting menu. Palette swapping is only an aesthetic option in the game.