The first thing to do is decide which color Jell-O you want on top and which one on the bottom. You may also want to cut the strawberries in half, unless they are smaller strawberries than you can leave them whole if you'd like.
Once you've decided on this you will make the Jell-O per the package instructions and poor it into a large bowl. Put in the fruit for that particular Jell-O color; strawberries for red, blueberries for blue.
You will then need to let the Jell-O start to set, it will not need to set completely, but it will have to start to set before continuing.
Once you have a partial set of the first Jello, you will then put the cool whip layer on. This can be as thick or thin as you'd like, but remember to make sure you have enough room for the 2nd layer of Jell-O.
Now you can make the 2nd batch of Jell-O, just as you did the first batch. The only difference is you will want to get the Jell-O slightly set before transferring it into the bowl with the other layers, otherwise it'll be to watery and will wash away the cool whip. You don't want it to set for too long otherwise you'll need to spoon it out and then it will not turn out right. Once you get the 2nd batch of Jell-O into the bowl you will add the fruit and then allow it to completely set. Usually a few hours.
You can make this dish the night before to allow plenty of time for setting.