1.Put out the Digimon you want to grow up.
2.Right-click on the miracle fruit, then confirm twice.
3.Your digimon has either: grown up, the contrary, or say at the same size.
4. For better chances, wait to have enough miracle (or goddess) fruits in order to use it all in a row, until you reach your desired goal.
Note: even if the size percentage stay the same, the effective size (and the statistics) can change. Check the size in the digimon window ("D"key).
Note2: a fruit of the goddess has fewer chances to reduce your digimon's size as a miracle fruit. So you'll have better chances by using first miracle ones to gain a few centimeters, then goddess ones when it has growned up 2-3% in order to prevent loss of that gain.
Note3: depending of its hatching level, a dgimon has a certain size range it can't surpasses.