moving folders around and editing code afterwards

[eluser]pendalpusher[/eluser]
currently I have my apps setup something like this


/Main Directory
/ci_apps
/my app
/application
/system

/webroot
/my_app
/index.php

I currently use dreamweaver to write code. So I need to make a different site for both the application and the actual website root. It gets very confusing.

Is there a better coding application for handling codeigniter suggested practices? Or do I just need to deal with it?

Thanks,
C