[eluser]TheFuzzy0ne[/eluser]
It depends. Do you use active record? MySQLi is virtually identical to the MySQL extension, the main difference is that MySQLi has been geared more towards OOP, whereas the MySQL extension is procedural. They essentially do the same thing, and you should ideally use them through CodeIgniter's database abstraction layer.
In theory, if you use the CodeIgniter's database abstraction layer, and no proprietary SQL statements, your application should work no matter what kind of database engine is running under the hood.