Pacing is a good balance checker I've found. Basically determine how long your game will be, and how many bosses you will have. Each boss should have a benchmark level that you intend the player to be, this should be an average level. So let's say your max level in the game is 99, in most RPGs you can beat the main boss at significantly less than the level cap (usually around 50-60). So let's make 60 the benchmark level for the final boss. Now let's assume your bosses are fairly evenly spread (they usually aren't but as an example) and you have 12 total, well that's easy math, 60/12=5, so you're expecting the player to advance roughly 5 levels between bosses in this scenario.
By setting up the level you expect the player to be at on average for the boss you can do several things:
-Balance that particular boss's stats against that particular level, keeping in mind that the player could be under or over levelled for that encounter, this is just an average.
-Balance the experience gains on trash enemies so that it takes a certain number of battles (on average) to reach the next level benchmark. (So you fight roughly the same amount of battles between each level up with smaller margins of error)
-Balance skill sets to be available only when you feel the enemy difficulty begins to call for it (like upgrading from a low level ot a mid level heal only when enemies are frequently doing that amount of damage)
Obviously this was a perfect scenario and most RPGs don't work that way, no big deal you can easily adapt it. For example if it took twice as long between Boss B and C as it did between Boss A and B, then you just double the level requirement in your pacing.
Defining your pace is going to be the trickiest, it depends highly on the level of grinding you want players to do. Generally if you want to minimize grinding, a good goalpost is to have the pace set at no more or less battles (meaning no running from battles) than what it takes to fully explore each area. So if you zip through an area ignoring side passages, and looking for extra loot, you will probably be underlevelled, if you intentionally pace back and forth through an area fighting more monsters you will be overlevelled. There's other variables to factor in there, but for the average RPGMaker length game, I think this is as good a rule as any to follow without going TOO complex.