You will need to keep track of where you are placing the files and adjust the paths accordingly. Since you can put the files into any folder or end destination it is very difficult to tell you what the correct values should be for the links, this is why it is important to have an understanding of basic linking structure so that you can make these changes when they are needed.
For the error you are currently getting when you try to visit the index page what is the path to the connection file on the top of this page? Also, where in relation to this file on your live server is this connections folder?
If you have moved just some of the files into this new subdirectory it may be the problem, ensure that you have uploaded all of the files and folders for this part. If it is necessary to share the private details I will open you a ticket but I think this is just a linking issue that we should be able to work out without these details.
