Before I start playing with the amp, are the user created presets stored separately from the inbuilt ones? I've read through the manual and got the impression that if I save one that I have created then it will overwrite the last one I was using?
Yes, saving a preset on the amp will overwrite the old one. But you can create a backup in your library or you can save the new preset on your phone- then you can use the Gateway-app to change presets on the amp.
Note that changing the settings of a preset wont be permanent until you actually "Save" the preset. then you can save it to a new location or your gateway app. That way you can keep the original preset too.
