Recently I just used Fantastico tool to install phpnuke in to server directory. But there has less themes and couldn't select nice looking theme. So I downloaded phpnuke themes from downlaod sites as zip or rar files. I know I have to upload those files to Themes folder under server directory...The problem is there are a few folders such as Doc, Images, Style as well as theme.php and index.html. I'm not quite sure how to upload those folders and file from cpanel. Would that be uploading files from File manager or any other ways to upload folders (with plenty of files inside the folders) ?

The best way to do that is with some kind of ftp manager,you open your "themes" directory on one side and you upload into this directory your unzipped version of theme, I think that when you unzipp your files you will have something like this:

1. Folder with your theme name;

Inside that folder yoy have a few more folders and files, so upload the whole folder to your "Themes" directory and after that you can choose your desired theme from preferences, when you log in as admin.

I hope, I've helped.

Good Luck!