You will need to setup the XBMC web server in order to use XBMC Commander.
Don’t worry, this is easy to do.
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System info

To verify that your XBMC installation is capable of being controlled by XBMC Commander, open the system information.
With the standard skin you can do this by going to "System", pressing the right-arrow key and selecting "System info".
Make sure that your XBMC version (that's the blue string to the bottom right) is at least 10.0

While we're here you can also note the IP address of your XBMC Server, we will need this later on.
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Network settings

Start XBMC, go to Settings -> Network -> Services

Make sure that:
  • "Allow control of XBMC via HTTP" is selected
  • If you want to secure your XBMC web server, choose a username and a password
  • Also note the port setting - 8080 is usually just fine. You might try to change this one if you experience connection problems.
  • check "allow programs on other systems to control XBMC"

If you experience connection problems, please verify
  • if you can open xbmcs web interface in safari
  • if windows firewall is blocking the xbmc port
  • if switching the xbmc port helps
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Set up your sources

In order to get the most out of XBMC Commander (and out of XBMC!) you will have to set up your media sources, set a content type for each of your source, and turn on library mode.

I won't go through this here. If you haven't done this before please follow the XBMC Quick Start Guide.
Just remember to set the content for each source.
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Set up XBMC Commander

Now it's time to add your XBMC Server to the XBMC Commander app.
Start XBMC Commander on your iPad.
If you have't already added a System, a window will popup (otherwise go to Options an tap on "add").
Now fill in
  • a unique identifier of your choice
  • the IP of your server (as noted in system info)
  • the port XBMC is running on (should be 8080 if you didn't change it in network settings)
  • username and password

You're ready to go!