Since a stored procedure is created, altered and dropped using queries you actually CAN manage them using phpMyAdmin.
To create a stored procedure, you can use the following (change as necessary) :
CREATE PROCEDURE sp_test() BEGIN SELECT 'Number of records: ', count(*) from test; END//
And make sure you set the "Delimiter" field on the SQL tab to //.
Once you created the stored procedure it will appear in the Routines fieldset below your tables (in the Structure tab), and you can easily change/drop it.
To use the stored procedure from PHP you have to execute a CALL query, just like you would do in plain SQL.