A domain, a couple sub-domain, & multiplte instances

[eluser]phusiondesign[/eluser]
Randy- I appreciate your help.

I am trying to do pretty much exactly what you just described, and I will use your setup. I reconfigured it that way now, but am having the same issue with the application not in the root directory (two/application). The index.php file at domain.com/two/ gives me the same error I posted above.

How do I reconfigure the index.php & config.php file to see the system folder?