Since you are saing your boards have not went well. Though it would far easier for me if you can quantify your X11 board result as then I could had answered your query lot easier.

But still I'm assuming that you have passed in all the exams and also be the top 20%ile in your respective board, then you have qualified for JoSAA counselling. 

And if my assumption is right then your board marks holds absolute no improtance in JEE result. 

Since your JEE advanced paper was good then I would suggest you to wait for the result and for the official key to release.

All the best