Move: Simply move sprite to X,Y position you want it to start. Then move to point in timeline you want the move function to stop, and click and drag the sprite to it's X,Y destination.
Scale: Click and drag down to decrease scale, drag up to increase. Choose beginning scale, move to endpoint on timeline, and choose a new scale to either shrink or grow the sprite over time.
Fade: Click and drag down to fade out, up to fade in. You need to set points on the timeline if you want it to fade gradually over time.
Rotate: Click and rotate to desired angle. Sprite will rotate in direction of your dragging when setting it to work over a period of time.
To designate the layer when you add a sprite, simply drag the sprite name listed (column on the right) to the desired layer section.
Removing a Transformation: Anchor points are demarcated by "white ticks" on the timeline. Choose the < or > arrows to move to each anchor point, with the transformation you want to remove toggled. Hit the - button to remove the anchor point. To remove the entire transformation, remove all the anchor points one by one.