In no particular order other than guaranteed order...
#1: UNOWN (one of each of the 28, and Baltoy & Claydol)
#2: DESERT (theme; Sandstorm related stuff, Onix/Steelix, Dunsparce, some fossils, Skarmory, Trapinchies)
#3: LEGENDS (5 Gen One, 5 Gen Two, 9 Gen Three, and 11 Gen Four (Manaphy, Phione, Heatran boxed elsewhere))
#4: Seafloor (deep sea fishies, fossils, Dratini, Manaphy/Phione)
#5: Seashore (ocean surface stuff, beachy things, shellfish and crustaceans)
#6: River (more water stuff with some inland stuff like Farfetch'd)
#7: Forest (basic Grasses, some bugs, Sudowoodo)
#8: Jungle (different Grasses, some bugs)
#9: Farm (farm animals, crop related things, some dogs and cats)
#10: Iceberg (Ice types and some Thick Fat and Clear Body)
#11: City (Psychics, Ghosts, and some Poisons)
#12: Sky (birds and flying Pokemon
#13: Starters (most starters, some boxed elsewhere)
#14: Volcano (Fires and some Rocks)
#15: Cave (Rocks, Zubat, Wobbuffet, Ursaring, Salamence, Sableye, Steels)
#16: Trades
#17: D.U.D.'s (stands for: "Daycare (projects), Unorthodogs (HM Slave Smeargle), and Dittto")
#18: ??? (stuff uncertain of where to shaft get put here)
Evolved Pokes are moved towards the box tops.