Yeah, there is no end to balancing until the game is completed and even then sometimes it's not done lol. I tend to test every part that I add into the game along with everything before it with each addition. This way I can get the idea of if things are too quick or too slow, too easy or difficult, etc. If I feel it's in a good spot, then I'll make the demo and pass it off to my dev team and testers and get their feedback. If they mention something is off then I'll go back and test it again with that in mind, often times realizing what they meant and fixing it accordingly. But yeah, one of the best ways to make this process easier on you is to know what you have in mind for scaling before doing it. Adjusting an entire game after it's complete can be extremely tedious and often the cause for abandoned projects (even with them so close to being finished). So my way is to do it step by step and test it as I go. This way I have everything in order and it all flows together with a nice difficulty curve as the story progresses.
It does really depend on your game's genre and style to determine what would need balancing and be able to fit with how you want the game to go. If you don't want to do balancing by using plugins, you can likely refer to some of the tools that Yanfly has linked on their website. Those tools include enemy paremeters, player parameters, and several other tools that will definitely make the process less confusing without the need for a plugin (but if you're using a standard RPG style to your game I'd highly suggest using plugins since they'll make it less time consuming and generally easier).