• Go through class 11 and 12 topics theoretical
• But have concepts cleared in mathematics
• Refer important topics which are mostly asked
• Solve all last year question papers

See it is not a messy situation. It is just a bit hard. So for starters, I would ask you to not get into a negative mode. Next it is not true that class 12 syllabus is based entirely on class 11. If that was the case then why would JEE Main syllabus include both the classes? See you may have to work much harder than the others. 

Check past year papers, Check weightage of topics that come in JEE Main. Study those from class 11 and for class 12, you go as per your school curriculum. JEE preparation means you have to seriously dedicate yourself from now on. And you can crack it. Learn a topic from each subject every week, revise till you get it right. Do mock tests to get strong in it. You will juts need to work without a stop all year through. All the best!