I suggest that you playtest your game, and keep in mind levels, playtime, and difficulty you want that certain part of the game to be at. If the tester or yourself feel or notice that a boss of a certain part of the game one hits all your actors, even after you gained more stats, however the monsters in that stretch of the game were where you wanted them to be at, then you obviously have a target to work on. Keep in mind also, if you were simply pressing attack throughout those fights, that you might want to rethink your battle system entirley esspecially if you were at what you and your testers deemed as the average level of that area. Unless you are deconstructing the genre. Or FFXIII.
You can fix those aftermentioned problems by also implementing a level scaling script, which will help solve some balance issues for the game. However at the same time you must figure out a formula for the level scaling so the difficulty remains constant or scales slowly upwards throughout the game. You don't want your game becoming increasingly easy or spiking into a wall as tall as the Burj Khalifa.
In the end, a outside program can not help balance the game for you. Your game has to meet your own standards of balance. Want a hard game? Well you got to balance as you see fit. Same for easy, a baby's first RPG, or a game akin to DnD. All have to be done with your supervision, it's the only way.