If I understand correctly what you're doing, I think if you turn off
AutoLayout on the diagramming toolbar, you can change just the one color.

If not, then I'd probably just draw the triangle pieces "freehand" using
autoshapes. Specifically, I'd use the trapezoid (drawing toolbar |
Autoshapes | Basic Shapes | Trapezoid) for the base of the triangle, use the
rotation tools (Drawing toolbar | Draw | Rotate or Flip | Flip Vertical) to
position the wider edge on the bottom, and then play with the yellow diamond
on the shape until it's at the angle I wanted. Then I'd duplicate the shape
and resize it as appropriate until I got to the top, where I'd add a
triangle.

Glenna's suggestion will work fine but you can apply animations to just one
part of a diagram also if you wish.

Apply the animation eg emphasis > change fill color and then in the custom
animation pane click on the little double arrow below the name entry to
expand the animations. You should now be able to see the individual
trapezoids animations?

Select and "remove" any animations that you dont want. If you repeat this
you can get different color changes for each trapezoid