If it were me...
I would run the panels through the planer or a wide belt sander, removing a bit off each face until they were the same thickness. I don't see an issue gluing them to a 1/4" panel. Wood is unpredictable, so you will be taking a chance. In my experience, anytime you glue something to one face you should also glue something to the other face to prevent warping.
If it were thinner you might get away with only one face being glued, but 1/4" is fairly thick. So, you would be taking a chance by gluing to only one face.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)