Quite a bit! To sit ON a stool is to be recumbant on a piece of furniture, usually comprising a base and three legs, built for the purpose -- and assuch not something you can sit IN.
To sit IN a stool is to find your posterior displacing the faeces of an animal or human being as it settles on a surface, usually by accident...
The confusion may arise from the fact that while you sit ON a stool you sit IN a chair... and that's a convention of the language which probably derives from the fact that while a stool is just base and legs, a chair has a back and perhaps armrests and as you sit in it it can feel like you're within something.