You have joined an institute for JEE preparation, it is good as they provide quality education as well as they also provide quality study materials which play a great role in your preparation. As you first three chapters are not completed , you may suffer a lot because in starting of the  JEE preparation all the basic things were taught by faculties which have a great importance in further.

But it basically depends upon which chapters you have missed, if you have missed UNIT AND DIMENSION chapter in physics then their is no problem. you can cover it later buy if you escape VECTOR in physics or MOLE CONCEPT in chemistry then you suffer.

According to me , the starting chapters are quite easy and relatable from our previous study . So its easy to cover it, So cover it  as soon as possible and go further.