As others have said, there is no one solution to this. Here's how I balance my games:
1. I lay out the game world, at a high level, and have a rough idea for the story. These are the MOST important, because THEY will drive everything else I say below --- it's how I make decisions of "How powerful is XYZ?"
2. I decide how much emphasis I want player level to have versus equipment. The more emphasis I put on equipment, the larger the bonuses it gives to ATK/DEF/MAT/etc. The more emphasis I put on player level, the more I grant special bonuses (such as multipliers to base ATK) to specific classes.
3. I decide how much damage I want a particular encounter to do to an optionally prepared party. A good rule of thumb is random encounters shouldn't take off more than 20% of the entire party's health because these are frequent, while boss encounters can take off 500% of the entire party's health (or more) --- meaning the player MUST heal during boss battles.
4. I make "best guess" values for the stats, including equipment, player level/class, etc. And I make similar best guess values for the enemy stats. The latter I do one at a time.
5. I use the very handy Battle Test button on the Troops tab --- a LOT. I prepare the party for battle and play through the battle. At the end, I see if it was too easy or too hard, and adjust some parameters. Which ones depends on what I want the enemy to reflect --- if it is a hard-to-hit but fragile opponent, I might set its EVA very high but give it low HP and DEF.
6. During playtesting, I make heavy use of Yanfly's excellent Debug extension. This has a Battle Test type feature, but since you're playing inside the full game, any battles you invoke will go against what the party has now. This is great if you're not relying on the traditional class/level way of granting skills.
But, really all of the balance decisions depend on what you want the battles to accomplish. If you want some to just be XP/Gold/Item dispensers, they don't need to be too hard. If you want some to be epic battles where the party is fighting for their lives, so be it. And you can even have battles where the party must lose.
So let your story drive HOW you balance your game. If your story says "Everyone struggles to survive," maybe your battles are rare but all are extremely difficult --- if so, you need to balance it so players aren't always dying. If your story says "Specific areas are dangerous," maybe they have super hard enemies, along with extra rich rewards for those who take the risks.
The excellent tips from other people and myself are useful, but in the end you're using all of these battles merely as tools to tell your story.