Now that Content Template is gone for Drupal 7, how do I modify nodes?

I will try both. Thanks again!

... Display Suite and Panels will do some of the things I need, but not all of them. So here's an example.

I know that in Content Templates, if I insert this code into the template for my "webcomic" content type:

<?php print $node->content['custom_pager_top'][1]['#value'] ?>

That it will display a custom pagers "link bar" for Help Desk (one of my webcomics) at the top of the node, but only in nodes within that content type that are flagged with the help desk taxonomy (that's the "[1]").

I know it will do this because Content Templates actually exposes all the different fields that are available for a Content Type, and after a little trial and error I was able to make it work.

Using Display Suite and Panels I can actually add that php snippet into the content type layout, but it doesn't work. It could be that Custom Pagers had changed the variables you're supposed to use, or it could be that D7 no longer supports modifying content type with php code in that way (i.e., I have to move it all to templates. Which will be fun). But there's no way that I can see to even check.

Likewise, using my original example in my first post (getting the book navigation links to appear on the top and bottom of the page), this is what I've done with Content Templates:

<?php if ($node->book['depth']==1): ?>

<div class="NovelBody">
<?php print $node->content['body']['#value'] ?>
<?php print $node->content['book_navigation']['#value'] ?>
</div>

<?php endif; ?>

<?php if ($node->book['depth']!=1): ?>

<div class="NovelBody">
<?php print $node->content['book_navigation']['#value'] ?>
<p><?php print $node->field_chimage[0]['view'] ?></p>
<div class="chteaser"><?php print $node->field_callout[0]['view'] ?></div>
<?php print $node->content['body']['#value'] ?>
<?php print $node->content['book_navigation']['#value'] ?>
</div>

<?php endif; ?>

Which does this:

- checks to see if the index page is displaying (that's the book depth equals 1 part). If it is, it only displays the bottom link (formatting and styling was simpler that way)

- if the index page is not displaying (that's the book depth != 1 part) then it displays the book navigation links, the image for the chapter, the chapter lead, the body of the chapter, and then the book navigation links again.

... I haven't been able to figure out how to make this work. I noticed that Display Suite contains a section where you can store code snippets, but it doesn't seem to make those available anywhere in panels, which gives you the most granular control over the page... and unfortunately the DS documentation assumes a lot more knowledge about the inner workings of Drupal than I have (and it seems to largely focus on Drupal 6).

So anyway. I'm still thrashing around. DS and Panels have taken me about 30% of the way to where I need to be, but I've got a ways to go yet.