The pages based on CMS Templates, are virtual pages.
any new page created from the template becomes the default page that will be loaded.
at the top of the page, right under the "Choose the content area you wish to edit below" is a "View This page" link
Click that link, and you will see in the address bar that there is a querystring variable:
template.php?Template=3
in my example, i created the template region as template, yours will be different.
This querystring variable is used to determine which virtual page is loaded.
to make the menu automatically populate with new pages template pages, you will need to edit the css menu writer menu contents.
In the main template, select the menu, then in the property inspector click the edit menu contents option.
Select the top level for your cms template page, then click the plus button and select Add New Dynamic Link.
set the table as pcms2_contents
set the label to ContentGroup
Set Key Column to ContentID
for the link, select the pcms template page, then add the question mark, querystring variable name and equal sig, click the plus button next to Add to link and select the ContentPageSetOrder column, as an example, my finished link would look like:
/template.php?Template=[ContentPageSetOrder]
Now open the CSSMenuWriter/cssmw_content/menu.php file, in the server behaiors section, double click the menuwriter_pcms2contents recordset, and change it to:
SELECT C2.ContentGroup, C2.ContentPageSetOrder
FROM pcms2_contents AS C1 LEFT OUTER JOIN pcms2_contents AS C2
ON C2.ContentPagesetParentID = C1.ContentID
WHERE C2.ContentPageSetOrder IS NOT NULL
GROUP BY C2.ContentPageSetOrder
ORDER BY C2.ContentPageSetOrder DESC
do the same thing on the index.php page to modify the home page navigation and edit the recordset in the CSSMenuWriter/cssmw_home/menu.php file