The only 'method' I use is by playing the Game, over and over. I'm rather in the minimalist camp (one could read that as 'lazy',and that's fine...); I'm not overly worried about having things 'exact'. My Enemies are rather the standard ones (Slime, Bat etc...); it's only really the Mini-Bosses that I customise. I just throw in whatever inspires me, try it out a fair few times, and adjust a little if required. If the Hero is too weak, he'll get whipped; if he's too strong, it's the enemy that cops it. That's as far as I take it.
I've a whole series of Enemies, in general, for random Encounters, and I chuck 'em in using Regions so as to have the strength I desire in the right places on the World Map. My enemies, such as Trolls for the Caves, are duplicated as Blue, Green, Red etc, each with a bit more 'punch' than the preceding one. I group them into Troops of one, two or more, so there is a whole range of enemies to be encountered. I don't find it critical to have anything more refined than that; there's a factor chance involved, and if things get tough..? Well, the Hero had better stock up on Potions, that's all. I keep it simple, by necessity as much as anything else.
Disclaimer: I'm lousy at Games, myself, and find few folks willing to go to the trouble of testing out my stuff, so I tend not to waste my time over-thinking these things. It is what it is.