I am thinking of setting up a sub-domain on my website more specifically a help section, is a sub domain better for back linking to the home page of the main site than linking from an internal page say three levels into the website?
Taking a look at this from Google's perspective, they believe that subdomains are important when there is a logical reason to have one topic covered in a subdomain compared to a page on the same site. So, if you are going to focus on only one topic on the subdomain ,you could see that get ranked. However, it will still be treated like a top level domain meaning, if you want it to be ranked, you'll still have to get links pointed to it.
Nice one, the subdomain will be a sort of F&Q and help section focusing on the same topic as the top level domain, this should help a little with our rankings in google over time of course.