I've finally been able to put some time aside and have a go at installing Comments Plus.
From my comments.php I have found that the hook for me theme is:
Strangely it seems to be the same for the start and end.
Using this hook in both the options on the plugin page, Comments Plus does show up, however there are a couple of problems I have noted so far:
1) Comments that are already on the post are no longer showing.
2) Comments plus is also showing up on my homepage below the titles of certain articles (it seems random)
I have turned the plugin off for now, and am wondering if we can arrange a time where I can switch it on so you can have a quick look at it and see what the problem could be.
I look forward to hearing from you soon.