Balancing is relative. Enemies' stats only make sense in context with actors' stats, the number of actors, and the damage formulae of available skills.
My suggestion is to fix these things one at a time. Since there are (usually) fewer actors than skills, and fewer skills than enemies, it makes sense to fix them in that order; then you can have your first dungeon entirely finished and playable, and still have room to add new late-game enemies without risking unbalancing what you've already created.
I'll use my own project as an example. (Sorry, no link yet; I'd like to get a bit further before I start a project thread.)
I had thought up a magic system with six elements, so I knew that I wanted there to be six actors, one for each element. That fit in great, because there are also six battle stats; so I laid out a grid, and gave each actor a rating "1" to "6" for each stat, ensuring that every actor had one of each rating. I knew I wanted to use low numbers, so I made a "3" rating correspond to a stat value of 10, and each step was +2 in the case of Attack, Defence, Magic and Magic Defence; +1 for Speed and Spirit. For HP and MP, I just summed each character's physical ratings (for HP) and magical ratings (for MP) and multiplied by 8.
Now, for the first dungeon of the game, only one actor is available, and my grid system gives her initial stats of 32 HP, 32 MP, 12 Attack, 10 Defence, 16 Magic and 6 Magic Defence. (I decided that each stat increases by 2 on level up, but that's not relevant for the very first battles.) It looks silly if the starter weapon and armour have +0 stats, so I gave both +2. (Erika's effective ATK and DEF are 14 and 12.)
Since I'm working with low numbers, I decided on a damage formula of 2 x ATK - DEF.
Now for the enemies. Each one has a different role in combat (especially for the tutorial dungeon), so each needs to have stats suited to its role:
Roach. For the very first "how to fight" tutorial, the monster needs to go down in exactly two hits (so you can see it hitting the actor), and its one hit on the actor needs to do noticeable damage, but not enough that the player gets worried. I gave it 2 DEF because it's nice to see (relatively) big numbers come up for your damage on the enemy. That means Erika hits it for 28 - 2 = 26, which can be 21 to 31 with variance. So the roach gets 40 HP. Its ATK is 10, so it does 8 damage to Erika. Its magic stats don't matter.
Wood Golem. This monster is intended to teach "some monsters have strong physical defence, so you should use magic". Because this will work within my story, I did this by having a guide follow Erika in the tutorial dungeon, and he explicitly states you should use magic on the Wood Golem, and tells you about saving right before the battle. So I felt okay with magic one-shotting the Wood Golem (it's weak to fire), but if you ignore the tutorial and use a physical instead, it gets a turn, and can one-shot the player. This allows the monster to show up in pairs or larger troops in the second dungeon, when Erika is a bit stronger and you have a second party member.
At this point I tried out some different troops. Roach + Wood Golem is fine as a lesson on eliminating the greatest threat first. Two Roaches work as a lesson on using healing items mid-combat (and giving the player a little confidence boost: you can actually defeat a troop that outnumbers you). Three Roaches are simply too much for a solo Erika, so forget that, but make a note that three (or four or five) Roaches may be an interesting troop for the next dungeon.
Slime Cube. The other thing I wanted to teach in my tutorial dungeon is Erika's Fire Blade ability, which buffs her ATK. For this to be effective, I need a monster that can't be one-shotted normally, but can after a single buff; then a troop of two such monsters can be defeated in three turns with Fire Blade, four without. I can't tweak the Roach for this, because then the player would have a legitimate complaint "why didn't you teach me this sooner?" So, new monster. It must have less HP than the Roach, so let's make it all-round weaker, with 1 DEF. After a single buff, Erika's effective ATK is 17, so she hits it for 34 - 1 = 33, which can be 27 to 39 with variance. But if I give the monster 27 HP, Erika has a 50% chance of one-shotting it without the buff. So let's compromise and give it 30 HP. That means that with the buff, Erika will usually one-shot it (10/13 chance, to be precise). Because of that uncertainty, the monster needs to have lower ATK as well, so that bad luck won't kill the player.
For later dungeons, it gets more complex because there are more party members, but it still comes down to the same ideas: How many turns do I want this enemy to go down in? How much damage is the party doing per turn?
Of course, the first dungeon is the easiest to balance, because you know the player's current level and skillset exactly. Later monsters may feel balanced when you test them, and other players may complain about them being unbalanced, because they made different choices about building their party. All you can really do there is make a few tests with different builds, and be open to feedback from your testers.
...and saying all that took a lot longer than I expected. I wonder if I should expand this into a proper tutorial post?
