I develop my websites on my main server and then transfer the files to the server that the domain of the new site is on. I’m assuming the new server would required CodeIgniter to be installed on it? And if this is true, instead of uploading the entire CodeIgniter application into the root directory of my domain, making it more confusing to edit my site further into the future, would I be able to put the files I created in the root directory of my domain with the CodeIgniter application in a seperate directory?

You could put CodeIgniter's system directory wherever you want, just make sure the bootstrap file (index.php) links to it correctly (with $system_folder) and that you have the right permissions set.

  |-system  -\
  |          |-cache
...        ...
  |-wwwroot -\

$system_folder = "../system";

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