Great start! It seems a lot of people find the squats too easy in the beginning. Some people substitute more difficult squat exercises and that's fine, but if you want my advice, and you didn't ask :wink: but I'll give it anyway, I believe you should do the program as shown. When you start adding more difficult squat exercises, it's possible that you're taking energy away that can be added to the upper-body exercises where you need more intensity. If you're burning energy on jump squats, you'll have less to devote to pull-ups and push-ups, your admitedly weaker areas. Once you progress you can move on to the more difficult versions of the exercises.
If you want to add squat exercises after, that would be the best time, in my opinion. You could add a session of Tabata squats. That's where you do squats for 20 seconds as fast as you can, then rest 10 seconds. Repeat for 8 rounds. Your score is the lowest number of reps you complete in a round. Try to beat your record.
But I'm sure other people see results doing exactly the opposite of what I just said so you know, try it both ways and see which one you like better.