Setting Up Two CI On One Server

When you say second app, do you mean a completely separate install of codeigniter? 

If so, is it absolutely required that you use 2 folder with CI in it?

It seems like your solution might be a simple change to the routes file. It will also remove the need for 2 codeigniters for 1 application.

Codeigniter is simply one of the tools you need to learn to be a successful developer. Always add more tools to your coding arsenal!