Best practices for loading Code Igniter with existing EE install?

[eluser]Bruce Brown[/eluser]
Hello,

I've been working with EE for about a year and a half and now, in preparation for EE 2.0, want to load Code Igniter on my EE server. I see I can rename the index.php of either or both, so I can load them along-site each other. Can anyone suggest any best practices for co-locating EE and Code Igniter?

Bruce