I happened to be browsing some of the webcom Q&As on their services and found an answers to questions I would never have expected to be asked. And I did not like the answers.

      The first thing to know is that the most important thing you can do to maintain your site is have an exact mirror of it on your computer. That means every file and every subdirectory exactly as it appears on your site. That means that if it were not for the speed being different you can not tell if you are looking at your site on the server or on your machine.
      Why? Most people should be thinking, why didn't I think of that? First off you can develop and test your site faster. Or course if you are like me there will always a be few things that are not obvious until I see them on the server but I do catch most of them before uploading to my site.
      Another value is that you have a complete backup for your site should the server crash or if you should change servers. I have changed servers and expect to do so again. This way all I have to do is create the subdirectories on the new server and FTP the entire directory. The time it will take will be limited by the transfer rate alone.

      And of course the most repeated and most ignored advice ever. Back up your files. And if your service provider permits it, make a backup on the server and save it on the server. Disasters never come alone.
      Don't look at this as an arduous task. If you are familiar with PKZIP the switches are -ex -r -f to save all your files and subdirectories and restore them all just as easily. There will be similar utilities on the server you use. Ask root or webmaster about them.

      Although it is popular there is no reason in the world to have a separate directory for graphics. I have no idea why it became a popular thing to do. You can have the graphic in any directory you want and simply refer to it.
      I bring this up because it is a needless complication for graphics used once to put them in their own directory. Even for those used more than one, they can be referenced from any subdirectory on your site from any other. And a third point, graphics that are commonly reused are usually so small that repeating them in a subdirectory.
      As your site grows it is going to get complicated. The effort of making changes to it will become greater and the more mistakes you are going to make. Plan ahead to make it easy for yourself.