OK a bit of progress here but still adding to the confusion.
This is the important bit:
Am I better to just build a new WP store from scratch using the Factory & Views section and then just copy over my existing content and images that I already have in the website and placing them into the modules or should I keep the existing store that's currently online and just merge everything together somehow?
The other problem I now face is that apart from the categories and products the store does not seem to upload to my server. I receive no error message at all. If I check the URL there's nothing there.