If you upload files to the server and the server already had files of the same name in the location you are uploading to, those files would be overridden by whatever you uploaded. It may be helpful for you to think of your mysite.com directory as your live website that everybody sees. I personally would create a sub-directory such as dev.mysite.com to have a testing ground before you transfer things to your live website.
Always have local backups of your live website and databases and your development work. I have a local web server set up on my laptop so I don't really use a dev site. I just upload whenever I finish working on something and that way I always have the most up-to-date copy stored locally. If you use windows you can get wamp. There are similar stacks available for mac and linux (mamp, lamp) that makes deploying apache, mysql and php on your home system easier.
Actually learn about authoring for the web a little. Maybe google some html basics and what not. I am constantly amazed that people actually shell out money for hosting and don't know step 1 about doing anything.