I am not able to find where to write the stored procedure in phpMyAdmin and how to call it using MVC architecture.
you can create a stored procedure in the sql query window on the phpmyadmin as you write any other query. And as soon as you execute the SP, it will be stored in the database's information_schema. You can check the existence of SP by the following commands:
SHOW PROCEDURE STATUS
SHOW FUNCTION STATUS
and
SELECT ROUTINE_NAME
FROM INFORMATION_SCHEMA.ROUTINES
WHERE
ROUTINE_TYPE="PROCEDURE"
AND ROUTINE_SCHEMA="dbname"
;