You can add user-level customizations to the iPython shell by editing the following file in your home directory.
~/.ipython/profile_default/ipython_config.py
The file is not created by iPython during it's installation, so if it doesn't exist you need to create it. If you don't have it execute the following:
ipython profile create
c.AliasManager.user_aliases = [("cl", "clear")]