Spray a 9 x 13 glass baking pan with baking spray. I don't like using this stuff, but I think it's necessary to have Jello that separates from the pan in the end.
Place the rainbow flavors of Jello in 6 separate bowls. Use 2 small boxes of Jello per bowl. Work with one flavor at a time. Don't try to make all the flavors at once as the Jello will solidify as you work. (personal experience) Mix 1.5 cups boiling water into the first bowl. Stir 2 minutes until dissolved. Pour 1/2 the red mixture into the prepared baking pan (it'll be a very thin layer but should cover the bottom) and refrigerate for 15 minutes. I found setting my oven timer for 15 minutes helped me keep track of all the 15-minute intervals. While the first layer is chilling in the refrigerator add a heaping Tablespoon of Cool Whip to the remaining red Jello. You don't want too much Cool Whip as your layer will be too pale, but you do want enough to make the layer opaque. I found the heaping Tablespoon to be sufficient. (note: you can also use lowfat vanilla yogurt or sour cream instead of Cool Whip to make your layer opaque)
The more room temperature your Cool whip the smoother the layer will look. This Cool Whip started out frozen so I whisked it for a few minutes to make it look less chunky. (I rarely plan ahead enough to let things thaw before baking with them) As I worked on each layer the Cool Whip thawed and became easier to work with.
When the first layer is chilled enough to be firm but still tacky, pour the red Cool Whip layer to the top. 2 notes: 1)Don't leave the layers in longer than 15 minutes. This will cause the layers to be so firm that they won't stick to each other and will cause the layers to slide off each other in the end. 2)Pour the mixture onto a spoon to elimintate the stream from breaking the surface tension of the privious layer. This will eliminate a hole being created into a layer.
When the opaque layer is added to a color and put in to chill for another 15 minutes this is the time to mix the Jello for the next color. This gives the Jello time to cool down before adding it to the next layer. If the Jello is too hot when pouring it will melt the previous layer.
After you repeat these steps for each layer (12 total...see I told you you'd be in the kitchen all day) put the final product in the refrigerator to chill at least 2 hours. I left mine in overnight covered with plastic wrap.
This is what it looks like when you cut into it.
This it the end result.