Under "Configuration", you need to have enabled features "MOTOR_STOP" and "Disarm motors regardless of throttle value" both enabled. Otherwise, the value you select for Minimum throttle will be the speed that the motors will spin at when you arm the craft...however, you still want to set this speed to the minimum speed (value) that the motors all spin at the same speed, which you need to find AFTER you have performed a good calibration. It might take a few tries to find the sweet spot. Take your time.
CALIBRATION PROCEDURE
-Go to Motors tab.
-Have your Transmitter turned off, battery unplugged (but ready)
-Have props removed, then click "I Understand..." (DON'T LIE!! Take the props off!)
-Turn the "Master" slider up to max.
-Plug in your battery to the quad.
-Listen for a little tune of beeps, then wait for a pause.
-Bring the "Master" slider down to minimum.
-Listen for another confirmation tune of beeps, once it stops, the ESC's are calibrated.
-Unplug the battery.
Next, before changing and saving the other values below these features in the "Configuration" tab in the Cleanflight GUI, you should perform an ESC calibration to accurately optimize it to your setup, which will most likely always be different from someone else's numbers.
The specific numbers that you input for Min_Throttle will be relative to the actual values that Cleanflight sees from your Transmitter, located in the "Receiver tab.
This should be the lowest speed at which all your motors spin together (too low, and they will twitch, too high, and it will be too much thrust).
Middle Throttle
Set to 1500, Regardless of your receiver's raw values in Cleanflight.
Maximum Throttle
Set to 2000, Regardless of your receiver's raw values in Cleanflight.
Minimum Command
Set to 1000. Regardless of your receiver's raw values in Cleanflight.
Take note of your raw minimum and maximum values from your transmitter, get this from the Receiver tab.
Go to the CLI tab, and the minimum range and maximum range of your sticks needs to be set, so you can properly arm the craft for flight.
(Below is my personal example, change these numbers to match yours. My min travel is 1164, my max is 1834 on my Spektrum Dx6, using DSMX.)
set min_check 1170
//This is the value that Naze will use when looking for a value below zero (throttle) on the sticks, when trying to arm.
set max_check 1830
//This is the value that Naze will use when looking for a value at, or above maximum (yaw) when trying to arm, if you don't have a switch set to arm.