That makes sense, so each time the arduino asks the controller if it has x y z string waiting for it?
The Arduino is a server, when running your code. It doesn't ask anything anything. It responds when asked.
What might be confusing is the nature of the questions asked by the clients. What a client is asking the server is "Can you do something (with this data)?". That isn't really any different from the client asking "What is the temperature?" or "What are all the URLs on the Arduino site containing "PROGMEM"?" The supplied data doesn't change the fact that the client is asking the server a question.
I'm using 'if' statements to check for certain strings, and they will only be true once then the string will be gone
If you mean that the if statement will only resolve to true once per client request, that is probably true. The client data doesn't go away just because you checked whether it contains a particular string, though. So, I'm not entirely sure that I understand the question.
I hope that makes sense, maybe I am being daft and over complicating this matter?
I'm not sure that either assertion is true. Without seeing what the client asks, it's hard to understand what you want to do. From looking at the server page, though, it appears that each request from the client is a separate event, not something that could be used to put together any kind of animation. That is, the client request defines one frame of a movie, not a whole movie.