Need abit of clarification with a few things.
1) my original domain is
www.witguides.com do I use the two dns servers from this site for my Addon site
www.ebook-engine.com.
Yes you ensure both those servers are in your account.
2) Do I publish my site with the same IP address and same user name/password but use file- public_html/eboook-engine.
Yes
3) I was able to publish my files to ebook-engine.com but after a couple of hours they would be changed to
www.ebook-engine.witguides.com, do you know why this would happen.
I can only imagine you published another page by that name over your previous page ... this is all that comes to my mind, someone else may know something further on this.
4) Then the new domain
www.ebook-engine.com was blank with my directory page.
Yes sounds like what you did when you tell me this. You published witguides over your index page .... this is what I believe possibly happened. I suggest you republish the page that you saved as index and this should correct this, keeping in mind you will have to republish your other page by its new name ...
Your help would appreciated.