Congratulations for having interest in growing many fruit trees. That is good. Trying to grow them in a way that keeps all the trees happy is the next thing. If you dug a hole in the sandy beach shore to make a swimming spot, the water that you put in it would just drain away through the sand. But, if you placed a one foot thick layer of your clay soil on top of the sandy hole, the water would be unable to drain away and the swimming spot would work. Although the water would not be clear.When you water too often, or when heavy rains won't go away, the fruit tree roots in your dug-up clay hold excess water for a l o n g time, which is very unhealthy for many kinds of fruit trees. As an immediate action, I would not put any water on the plants without checking the moisture in the soil a few inches deep. If it is moist below, leave it alone until it is not wet.. For a "fixing" of the problem, when your next Winter is beginning, you could carefully dig up each tree's root ball and replant it ON TOP of the clay and surround it with a mound of good/organic/sandy/rich soil mix. Like a doughnut with a doughnut hole. Make the mound a little higher than the root ball, since it will sink downward as it settles. These mounds have the exact opposite challenge in that the water easily descends through them to reach the flat clay surface below. Keeping this mound moist in hot, dry Summer will take frequent, slow soaking to get them thoroughly watered and thus welcoming to the tree roots' expansion in search of moisture and food while enjoying what they did not have enough of before: air in the soil mix. As the trees grow in size, you could add more soil mix over time to enlarge the mounds. When the trees are ready, they can choose to send their roots downward into the clay below. Building boxed sides or some other kind of material for sides is not needed, though it may be wanted.