I am not able to find where to write the stored procedure in phpMyAdmin and how to call it using MVC architecture.
In phpMyAdmin you can create the stored procedure in the SQL window.
You may have to set the delimieter to something like "$$" instead of the default ";". You can change this from the bottom of the SQL window.

Also you can refer this: http://www.mysqltutorial.org/mysql-stored-procedure-tutorial.aspx