I really should get started on my stating guide I've been planning to do. Anyway, a few tips.
Attack and Strength: Both increases attack damage. First, decide how much more damage you want the actor with the weakest armor to take compared to the one with the strongest armor. Do you want robe clad wizard to take 150% the damage the steel clad warrior takes or maybe 200%? Adjust the Attack stat of the enemy until that ratio is accomplished. When you have done that, adjust Strength until you get the damage values you want.
Both Attack and Strength will affect how much damage an enemy does. However, Attack will also determine the ratio of damage between characters with high Physical Defense and characters with low Physical Defense while Strength does not. For that reason it's better to first adjust the Attack stat and then Strength rather than the opposite.
Intelligence: This stat does for magic what Strength does for physical attacks. Once you've given the enemy an appropriate spell, you can adjust the Intelligence until the enemy does whatever damage you desire.
Agility: This one is easy, decide when you want the enemy to act and decide an Agility stat thereafter. If you want it to act before the slow fighter, but after the nimble thief, the enemy should have an Agility score somewhere between that of the slow fighter and the nimble thief. Just note that there is a random variance to turn order.
Agility does other things than deciding turn order, but turn order is the most crucial function of it. The exception would be if you give an enemy an Agility based skill. However, unless you know exactly what you're doing, don't give enemies Agility (or Dexterity for that matter) based skills.
Dexterity: Has an usually minor effect on accuracy. As long as the enemies have a Dexterity score somewhat close to the average Agility score of your characters, you will do fine. You can just wing it. Let's say that the average Agility score of the characters is 60 when they reach a particular area. You can just go "hmm, let's give the quick wolf a bit more dexterity, say 80 and the clumsy golem 40" and you should be fine. Heck even if you screw up and accidentally swaps those stats, chance is the player will never notice anything. Dexterity really is the white elephant of RMXP stats.
Physical Defense, Magical Defense and Hitpoints: Let's say that the enemy takes 100% damage if it has zero Physical Defense. With a Physical Defense equal to the attacking character's Attack stat, the enemy will take 50% the damage and with a Physical Defense twice off the attacking character Attack stat, the enemy will take no damage at all. For values between, you will naturally get damages somewhere between as well. Magical Defense works the same way (as long as you set the MDEF-F of the spell to 100) however you compare Magical Defense to the Skill-Power of the attacking spell, instead of the attacking character's Attack stat.
Decide how much percent damage you want the enemy to mitigate and choose Physical Defense and Magical Defense thereafter. Once that's done, adjust the Hitpoints of the enemy until it survives as long as you want it to.
Evasion: How often do you want the enemy to evade an attack? Assume that enemies with high Agility scores evades about 10% more often their Evasion score while enemies with low Agility scores evades about 5% more often. Choose you evasion score accordingly. If you don't want the enemy to ever evade (let's say it's a big slime and you think nothing short of miraculous clumsiness would ever let you miss a big and slow slime) then give the enemy a big negative evasion score.
Now what you need to do to make the enemies as difficult as you want is to decide both how many blows they are supposed to survive and how many blows they need to kill the characters. Experiment until you find what works.
