The File manager will not go to files or folders bellow the upload folder you set.
if you want to be able to browse to files in your entire site, you will need to set the upload folder to the site root.
In the HTML Editor instance, you can edit the preset, and on the General Tab, in the file upload section select the Show Directories in file manager option, this will allow you to browse to other directories, when you wish to upload a file or image, you can browse to the desired target directory before uploading.
