To properly place SoT you should sort your mod list to look similar to this one.
The Skyrim Unofficial Patches order is taken straight from their Nexus page.

Note: If you use OBIS (Organized Bandits of Skyrim) you MUST place all OBIS files under SoT.

The following is (basically) the proper load order:
Skyrim.esm

Update.esm

USKP

Dawnguard.esm

UDGP

Hearthfires.esm

UHFP

Dragonborn.esm

UDBP

[Other ESMs]

Official hi-res DLC *Best to not use any high-def packages in script heavy modded games

UHRP
SleepingDangers-SandsofTime

[Other ESPs].....
.....

.....
SoTAntiCDT

SoT addons

SoT patches

Bashed patch (if used)

OBIS (Optional, but highly recommended)

OBISDB (if used)

Specialty followers (such as Vilja by Emma or Inigo by Smartbluecat)

AI Limit Increaser (always load at ABSOLUTE bottom if used--not needed if SoT is installed.)