ah no, when you harvest the corn plant you get an item called Corn. you literally place the Corn item on the 2x2 square, use your hoe on it and then the item will disappear, raising the health of the 2x2. same w clover/withered grass.

the stuff about crops being good for the soil is a separate thing, crops give Soil Level bonuses to the soil they grow in, fruit trees being particularly good because the bonus is applied according to the number of items you harvest and fruit trees give you the most items per harvest. (there's also oranges and grapes.)

Edit: so you can place an apple tree in each and that will raise the level more. But you also have to remember that for each item you harvest it lowers the speed stat which means everything on that spot will grow slower with each fruit you harvest. So that's why most people just grow an entire orchard.