Sorry for the delay in replying to this. Just wanted to update this post.
Ok so it looks like the joystick inputs, Start, Select and Buttons A and B cannot be skipped but once I get past those inputs I can skip away and save the config (by getting to the end).
So I just took some spare buttons I have and plugged them into the encoder and then once they were mapped I removed the psychical buttons I don't want leaving only one in my case.
Thanks to Mitu for the help