I read somewhere that the manuscript should be free from page numbers when uploading.
So do I include page numbers in my contents page or do I leave these off as well?
The manuscript can have page numbers in it. You may have been reading an eBook upload guide (such as kindle) where page numbers are meaningless.
In print editions you should include the page numbers as what you put in will be what is printed on the pages.
Hope this helps,
Perfect cheers Oliver