Ok, so if I change the gain on the desktop editor say down to -9dB, that amount of gain will be present when I plug it into the ipad? Does the gain selector on garageband modify this level of gain (as you would using the volume input on windows) or multiply another level of gain on top? e.g. -9db multiplied by XdB? Either way I managed to get some sound out of my guitar so that's a good place to start.
I don't know exactly what GarageBand does. It may use the i2Ms volume control, or it may simply apply another level of gain on top.
If you enable "exclusive" volume control on the i2M editor, the volume/gain you set (e.g., -9dB) can't be changed over USB (other than using the editor), so this gives you the best way to set a fixed gain without worrying that it will be changed. Windows, and OSX remember the volume setting you use, so each time you connect the i2M it will set the volume back to this level -- often this is useful, sometimes it's not. That's why "exclusive" mode was added to bypass this setting to ensure you always know the level is set correctly. So I suggest you enable "exclusive" in the editor.
However on the MIDI front, the ipad (or garageband) was making a bit of a racket when I was using the MIDI signal. I was using chromatic mode with a grand piano and the i2m was not tracking my notes at all. At times I would repeat the exact same notes but different ones would come out to the previous ones. It seemed to do the same thing with the bass guitar emulator and pitch bend mode. Do I need to alter some settings on the desktop editor?
You shouldn't need to adjust settings on the editor -- the default settings are good. Most problems are caused by playing technique, and learning to play a little cleaner than normal. Please see this video for a quick overview of what you should and shouldn't do:
http://youtu.be/0YGMZs72Gmk