With the JoomTools jtfileupload plugin life is much easier. If you want a simple custom field to upload files to a predefined folder without any knowledge about the folder structure and additionally want to protect your files, JoomTools jtfileupload plugin is your friend.
With the Joomla! core custom field media you can already create a field to upload files and link it in your articles. But it uses a pop up modal where you have to navigate to the destination folder and then choose the file you want to upload with the file explorer of your operation system. Then click the upload button, wait for it, then you have to choose the uploaded file and then you can insert it into your article.
You can define the destination folder and if you want to protect your files on creating the field. Your authors don't need to know where to put the files, they just need to choose the file and save the article and all work is done automatically.