The new version of phpMyAdmin (3.5.1) has much better support for stored procedures; including: editing, execution, exporting, PHP code creation, and some debugging.
Make sure you are using the mysqli extension in config.inc.php
$cfg['Servers'][$i]['extension'] = 'mysqli';
Open any database, you'll see a new tab at the top called Routines, then select Add Routine.
The first test I did produced the following error message:
MySQL said: #1558 - Column count of mysql.proc is wrong. Expected 20, found 16. Created with MySQL 50141, now running 50163. Please use mysql_upgrade to fix this error.
Ciuly's Blog provides a good solution, assuming you have command line access. Not sure how you would fix it if you don't.