when you are preparing for competitive exams like JEE you should try to cover the entire syllabus thoroughly, because anything can be asked in the question paper. Any standard of questions might be present.
Some of the most important chapters are -
1.) Physics- Rotation Electrodynamics Geometrical optics Modern Physics Thermodynamics
2.) Chemistry- Chemical Bonding Electrochemistry Reaction Mechanism Aromatic and Carbonyl compounds Coordination compounds Chemical equilibrium
3.) Mathematics- Coordinate geometry Definite integration Functions and Inverse Trigonometric functions Vectors and 3- D geometry Differentiation