In my manager, under Resources -> Chunks, I have a chunk called "Comments". In fact, it is a default chunk, installed with the default 0.9.5 installation if you chose to install the example content.
If you have that, just put {{Comments}} at the end the content for each document you want comments on.
If you do not have the Comments Chunk, Make an new chunk called Comments and put this in the code area:
<div id="commentsAnchor">
[!Jot? &customfields=`name,email` &subscribe=`1` &canmoderate=`Site Admins` &placeholders=`1` &output=`0` &guestname=`An anonymous visitor` &subscribe=`1` ¬ify=`2` &subjectSubscribe=`A blog you are moderating at scottydelicious.com has been updated`!]
<a id="pageComments"></a>
[+jot.html.subscribe+]
[+jot.html.comments+]
<a id="pageCommentsForm"></a>
[+jot.html.form+]
[+jot.html.moderate+]
[+jot.html.navigation+]
</div>
-sD-
Dr. Scotty Delicious, Scientist.