The OP has a good question that most of these don't answer. even if he reads all the tutorials he will be better off to solve the problem, but it won't answer it.
The problem is that Mario RPG(snes) is a 3D game even if not 3d objects. Also the game is judged in isometric and not 2D. Which also means that the platformer engine is useless. Actually using platformer will just make the entire project harder.
first read the basics, understand the manual. from there you will need to do consider these factors.
doing the mario rpg movement style will be a larger undertaking as a project than most others. it can be done, but get ready to do some trailblazing because your going to be moving into some seriously frontier territory.
movement will need to be custom.
you will need to add 3 new variables. World_X,Y,Z. then translate the world to screen position.
you might want to create a custom level editor and level loader and not use layouts for levels.
as for hitting the box. you need to work on a new collision check with objects stored in this 3d world. Either by an array or tree based system.