Two ways.

1. Manually arrange/move apps, by clicking menu button, then edit, then dragging apps.
2. Install appzorter lite from playstore. Has option to "compress" which will keep your existing order but fill in those blank spaces, or "sort" (alphabetically or by date I believe, and can put system apps before user as well in options).

2nd way alot easier, used to use it when I was on sammy based roms