In my humble opinion the only way to organize your shoes is by keeping the same type with the same type, that being said there is more to it to to make your life easier in the shoe department. It doesn’t matter if you have a walk in closet with an entire wall of shoe storage or just one little 8 pair shoe holder on the back of your tiny closet’s door, you want the shoes you wear the most to be the easiest to get to. So in the wall-o-shoes closet that would be at slightly below eye level, in the 8 pair shoe shelf at the bottom of your closet that would be on top. Both being the easiest to reach for spots.
Never keep the original boxes, I’m not going to say a whole lot more on this just please don’t do it. If you must have your shoes in boxes (which is totally understandable for really nice or expensive shoes or even if your closet is susceptible to a lot of dust build up) then you can purchase clear plastic shoe boxes for about a dollar a piece (even cheaper if you purchase these from amazon like the ones here). Trust me it will look so much more aesthetically appealing then seeing a bunch of different sized and colored original boxes all over your closet.
It is okay if some are out of reach, especially if you find yourself only wearing certain pairs on special occasions, so maybe just a few times a year, then it’s not that big of a deal to get on a stool and get them down. It will be much easier to do that a couple times then to cram all of the shoes into just the spots in your closet that you can easily reach.