Hello all. Started my guitar journey from Christmas at age 46. Really enjoying it. With all these exercises, and also when trying to playing the chords along with the practice songs, my left thumbs gets in all kind of weird positions. Also in this exercise.
How do you do it, or how to hold the thumb on the neck?
Greetings from Limburg, NL
This sounds weird. 
And, welcome to the forums!
Somewhere early in grade 1, Justin wants us to place the thumb on the back of the neck. There are two motives here: first is that is it the accepted good practice for getting hand position so that fingers can reach and move cleanly. Second is that it builds strength for a chord structure that you will see in (i think) grade 2.
It is fair to move the thumb around the back of the neck as your fingers need to reach from string 1 to 6. Top of the neck for string 1, probably just about center for string 6. It should not feel weird. It should feel like a bending of your wrist to bring your fingers around to let fingers bend and fret the strings.
If you can take a picture or two and post them, that will help. Mostly your fretting hand, but also try to give some way to examine the guitar angle relative to your body or shoulders.