Instead of thinking what will happen in JOSAA that too after JEE Adv, think what will happen if you dont even qualify JEE Main. (LOL)
On a serious note, JOSAA is a very simple counselling procedure, where after registration you need to set your preference according to your rank and are allotted seat accordingly in subsequent rounds of counselling.
For more information about JOSAA do follow the link below
However, now you shouldnt quite worry about the Counselling and Institute you will be allotted into. Keep your focus only on aceing JEE Main Attempts with a higher score each time and give a recurring performance in JEE Advanced.
For more information about JEE Main Preparation do follow the link below
For more information about JEE Advanced Preparation do follow the link below