There’s a lot of debate about where, exactly, to land on your thumb when in thumb position.
There are two main spots that people use, and each has advantages and disadvantages.
Spot #1 – on the knuckle

What I usually recommend people do is start just by touching the active harmonic right up there. Then once you get used to that, put it down on the active harmonic, and then move around a little bit. Over time, you’ll develop a callus, and your comfort level will grow.
jThe main disadvantage when we’re playing on the knuckle is just that your thumb kind of bumps into the other strings, so it feels a little bit less precise. Also, there’s something about the way that your hand is oriented when you’re on the knuckle.– it’s not the most comfortable for my fingers.
Spot #2 – by the nail

I like to get people comfortable playing closer to the nail. This is not as comfortable at first, because there’s this nice bone at the knuckle, and this side area is a bit fleshy. It can kind of hurt a little bit.
Ultimately, I find myself using both spots. It depends on the passage I’m playing, and there are many ways that you can get more comfortable using either spot.
Getting comfortable on the side of the thumb
First of all, just make it a daily practice. Do this a little bit every single day, and you will build up a callous.
You also wanna make sure that you are at a 90 degree angle, no matter what part of the thumb you use.
Finally, just make sure that the tone you’re getting with the thumb is as good as the tone on any other finger. So I play,
Don’t be discouraged, work at it, and comfort and skill will follow.