1.) Use FTP as mkdir() can have some weird results with respect to permissions
2.) Use a form, and make sure that if you insert into a database, that you do so securely (search on it).
3.) I'd set up a basic template. And give the user a chance to upload up to a certain amount of images. Then, each image will be displayed either on the right or left. Then, just insert the article and pictures into the template and save as the article.
My guess is you'll be using mysql or some other database for this project. Normal security precautions apply so make sure you escape all user-inputted data. As for securing a file-upload, you can limit what they can upload via MIME types, extensions, or reading the first few bytes of a file. Other than that, security for file uploads is dependant upon what they can upload...
~Brett