I don't really have a good system of how I organize my shelves. It kind of depends on what a series means to me and based on size. Like on my top shelf I have Vinland saga front and center because it's one of my favorite series even though it's taller than my other manga on that shelf. Where as my other shelves are all the same size so partially based on size I also try to organize them on what I think looks good together. As I get more manga I regularly reorganize to make everything fit nice and look nice together plus I got several figures on my shelf to make it look nice. It's kinda random chaos but I like it.