The rgb dot was use just as visual and doing reference to color, my bad for that.
Refill the ink cost a bit (25) and refill only the jar connect to it, to refill the pen you need to guide the pen to the jar (later you can unlock a button to refill the pen directly). The black square near the refill button is use to change the ink from the jar but you need to purchased them at the shop. If it's empty it's because none were purchased.
Almost everyone failed or struggle to get the game controls, i really failed to get the player to understand how things work but well, now i know why tutorial are really important even if we skip them most of the time XD. The user error you have experience is due to me not guiding the user through the first step, if my reply help and you have time don't hesitate to try again to reevaluate my game
Thanks for playing and sorry for the inconvenience