you will definitely be able to apply for JEE Mains exam upon clearing your compartment exams.
Yes,if you have cleared the JEE mains cutoff ,then their won't be any problem of compartmment exam.You are eligibile to take admission and attend counselling for JEE mains exam.You will get admission according to your rank and merit list.
Yes, a student with compartment in Class 12th board exam can apply for JEE Main Examination provided that he/she should sit in compartment exam and should secure at least minimum passing marks.
Refer here for more info - https://engineering.careers360.com/exams/jee-main
To know your other best admission possibilities of Institutes & branches in JOSSA & State counseling as per your percentile, You can use JEE Main College Predictor tool given below
Feel free to ask doubts in the Comment Section.
I hope this information helps you.