Thank you Pavel,
You are absolutely right, I have (with a clear head) got it up and running this morning, and I have to say it was straight forward - I think I was trying to over complicate it too.
So I did this following.
Installed ngCordova as instructed to on the web.
Ran bower install just to be sure.
Installed the sqlite plugin as instructed to on the ngCordova site.
Again ran bower install just to be sure
put the database initialisation code into my app.run
ran ionic run android
Used chrome to debug the app on my phone - all is working correctly.
Thanks all