To use the Hybrid Crop Generator, select the two crops you wish to mix together from the drop down menus to the left. The resulting plant will appear over here on the right side.
There are a total of 10 2nd Gen trees you can mix to make all 9 3rd Gen trees. Most of the 3rd Gen trees can be produced by mixing several different combinations of 2nd Gen trees together. When you have Tsurudan mix a 3rd Gen and if he's sucessful, you can name the new seedling anything you want.
Some combinations won't result in any 3rd gen trees. Combos like an Apaage plus a Mageramu will always result in another Mageramu. You can keep feeding Tsurudan those same two fruit (or seeds) but the result will always be the same.
Third Gen trees take much longer to grow than the 2nd Gen ones. It might take you 2 years before you'll be able to harvest the fruit of the super hybrid tree. The 3rd Gen fruit can be shipped via a basket in your Shipping Shed.