This is the crux of the issue I'm currently struggling with. I want each skill to have a niche, both in application and in advancement. For potions, that's alkahest and combat. For transfig, it's meridians and bonuses to progress. For herbology (since I've given enough away about it already), it's other skills' results, which is broad enough to stand on its own, or potentially a profit motive (it's been mentioned a few times that herbology can be lucrative). For charms it's manipulating the pool dice and... I don't really know yet.
As I've written it so far, a charm is a one-and-done object, but at the same time I want to have a way to incorporate bigger projects for Rei to tackle. The current fore-runner is a sort of banking system, where you can choose to add more to a charm, with progressively more impressive benefits at the cost of not having access to it until it's finished. Pulling that off, however, is proving quite tricky to me.
So for the moment, it's somewhere in between transfig and potions, which I realize isn't in any way a satisfying answer, sorry.
If you're open for suggestions: You could differ between internal use and external use. For now, both transfiguration and potions only affected yourself. Maybe charms are meant to affect your environment or your enemies? For example a potion or transfig which makes you more difficult to notice. By turning you to smoke or making yourself emit smoke which blurs where you are or somesuch. Charms could blur everything in a certain area for sometime, or make an enemy perceive everything in a blurry manner.
Another difference could be made between organic and inorganic applications. Potions could maybe used to harden wood or make it have some strange properties while it is unable to affect metal.
Just throwing some ideas out there, hoping that there's something in it that may inspire you
If nothing quite fits it's no prob 🤷♂️