Ok, I am glad to say that I have started working on my level again, and have finished the first planet!
Now, in "teleporters" the checkpoints have one animation, which fades in and out (with a controller). Anyway, in knytt stories, when you activate a checkpoint, the light sort of "flares", and gets slightly taller.
Within the data files, there is a file called "Checkpoint.png". This is the checkpoint image. There is also a second image called "Amplified Checkpoint", which contains and image of the checkpoint in the activated state.
It seems that this graphic is not used, and when the checkpoint is activated, it does not change graphic, unless It is an issue with the original version of saira (I have yet to update).
I am wondering how to make the game use this image, and change the image once the checkpoint is activated.