Links to zen cart directory index????

Hi, I successfully installed zen cart and have been working on the customization. I have found all of your previous posts very helpful. I could not find anything on this issue. After meesing around with the customization of my pages and adding a custom file (so that automatic upgrades will not replace all the upgrade work I have done) I must have screwed up. I followed the tutorial to the letter in adding the custom file for my index page, but when I now click on shopping cart from my webpage, or when i try to login to the admin page the index directory for shopping cart is displayed! I have modified my websites .htaccess file to stop the directory from showing so there is no immediate urgency, but I have no clue on how to begin fixing this! I could delete my customization page and have to start all over, but I would very much like to avoid doing this. Could you offer any help please??? Very much appreciated
Sincerely,
mikezuzia