What sort of file do I need on the server to send such to the Arduino? Sorry if this seems a silly question but the is all new to me.
If the requested file is in the web page directory of the server, the server will send it. If the request sent to the server requires evaluation to develop a response, then an application on the server takes the info sent to the server, processes it, then sends the info to the server for return to the client. I'm clueless to the php/mysql stuff, so you are on your own there. With my simple setups using windows/apache, I use a batch file or an exe as a cgi application to do stuff on the server pc, such as pan/tilt my web cam.