I have information I'm planning to sync between an iPhone application and a desktop application via a PHP script; is there a method of calling the script in the background to send data to the online database and then retrieve the data from the script?
See the URL Loading System and NSURLConnection. The "Related Sample code" on the NSURLConnection link may be helpful
If you wrap up all of your functions in a nice little class, you can use a method within the SDK to call a method in a separate thread. the method is called detachNewThreadSelector:toTarget:withObject:
Note if you don't want to do any processing of the returned data, than you can ignore this, and just use the standard approach to URL loading, as it is Asynchronous, and makes the connection in the background anyway, however the difference is that it's callback is called on the main thread (AFAIK). By executing in a separate thread, everything will be done there, so the UI will be free.
Also take care, the world of multi-threading can be long and rocky. Good luck