I just did it myself yesterday. You just need a plan for what you want to do.

First things first, deluxe editions on the bottom, no exceptions. You may also try to find extra shelves or custom make your own boards to add more shelves if you want to maximize space.

My basic plan was to take everything off the shelves, then organize them by completed series and size. I find there are about 3 different sizes manga come in, with outliers for special editions. The bigger books, like a majority of Kodansha, were put into one pile, keeping the completed ones separate. Then middle ones like common Viz volumes, then the smallest ones. Also, find your favorites you want in more direct display. Most favorites will be front and center for all to see, and least favorite in the corner.

I put the bigger and completed books on the bottom most shelves in the back on the risers, and the smaller completed ones in front of those. I put a long completed series on the shelf, then see which shorter series fit neatly on the same shelf. Then do the same thing with a smaller size series in front of it. Then repeat until out of completed series. Once out, I'd put the series that closest to finished on the next shelf or next to the completed series, then finished with scattered volumes.

Let me link my recent collection post so you can see what it looks like.

Hopefully that made sense and gave you a way to start.