Most of the time, they will correct themselves (this also helps them shed their helmet of a shell) and the roots will find its way down where the water is more saturated at the bottom of the pod. I have never seen roots grow upwards looking for water before.
However if you are worried she may not make it, you can always open up the cocopod a bit and set her up right before settling the pod back in. The top of the pod just barely need to be covered to block too much light from hitting the new roots.
Also keep in mind that if the pod is too saturated, the roots wont grow, they need to be looking for water in order to grow, keep it lightly saturated so that the bottom of the pod is heavier than the top.