I don't know much about patches on the shrubs but it caused by bacteria or fungi, which require certain environmental conditions to grow. Prevent or correct some diseases through proper cultural care, such as planting the shrub in the correct site, irrigating properly, and pruning during the...
Select a site with full sun and well-drained soil. Prepare the garden bed by using a garden fork or tiller to loosen the soil to a depth of 12 to 15 inches, then mix in a 2- to 4-inch layer of compost.
I was facing same issue, as you know dwarf fruit trees need to be planted quite deep, so it depends on how deep your raised bed will be. I would recommend you plant them in a pot, in a mixture of compost and garden soil, that way you could move them around if necessary.
I potted up my tomato plants, planted bizzy lizzies, pricked out my cosmos that were getting tall, planted some flowers in my wild garden and planted lettuce and cabbage plants.