You just replace the model you want to change with the one you want to use, keeping the right naming conventions of course.
ESF 1.2 doesnt have multiple transformations, but you can still use the models to replace the existing ones.
ie replace the /models/ssjgoku/ssjgoku.mdl with the ssj3goku.mdl, but make sure the name of that file is always named ssjgoku.mdl. Use the folder name as a reference.
Now when you go supersaiyan, you will be ss3 goku instead, although its only cosmetic.
ESF 1.3 Open Beta on the other hand, does have multiple transformation for most characters so far. So you have ssj2 and ssj3 mdls right? So put them in /models/ssj2goku and /models/ssj3goku respectively. Its a simple process.
When you select a character to play as, you should have a screen that tells you info about that class like what their attacks are, what stats they have etc. Here it will also tell you the powerlevel (PL) needed to transform, and by how much it will increase when you ascend.
Once you have enough PL, press the ascend button (Z by default, always check your KeyConfig) and you will transform. You will transform faster as your PL increases later on. To return to normal state, press the Descend button (X by default, always check your KeyConfig).
In ESF 1.2 you can only transform once. With 1.3 you can go further, you just repeat the same process, gaining enough PL needed and pressing Ascend.
!! Remember to backup the default stuff if you are modifying things !!