Hello.
In every college the admission is given on based of JEE rank only ( with the qualifying some criteria to be eligible for the admission I.e. percentage)
They will consider your highest of two marks and According to your marks your rank will be declared.
And counseling will be held.
So good luck.

Suppose a student has given JEE Mains both the times that is in January and in April. 

The admission would be given on the basis of marks scored higher than the other. For example a student has scored higher marks in April examination when compared with January scores then April marks will be considered and vice versa. 

Ranks are decided on the basis of scores so it would depend on them as to how they would give admission. 

If you still have any queries feel free to ask in the comment section down. 

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