Hi Erin,
Are you referring to links in the body text of your topic or links in the TOC (i.e. TOC entries)? If the project you were working on before was created and structured by someone else, it's possible that that wasn't clear to you that every topic is really a separate document. You
can create multiple TOC entries for a single topic with links to anchors in front of headings, but that is generally bad practice and we strongly recommend that you don't structure your projects like that.
If you want to link to a heading within an existing topic you always need to create an anchor -- this is the same whether the link is in the body text of the topic or a TOC entry. That has been the same in all versions of Help & Manual and has never changed. It is also not different in version 7. Without an anchor you don't have anything to link to inside the topic. Then the link will always go to the top of the topic.
I'm wondering if I'm meant to have a new file for each section that I might want to link to. In the past I used one topic file for each article.
Yes, if you are referring to TOC entries and not links in the body of your topic that is the way to do it. Each entry in the TOC should refer to its own topic file unless you have a very special reason for doing it differently (and almost always, you won't).
Also, if I need to use an anchor, is there a way to get the text of the header to show up for the cross-reference text and update automatically? That is, in the previous example, I want to have "chapter 3" show up automatically and also have the text "Here Is How To Do Thing 1" change in Chapter 5 if I change it in Chapter 3.
No, that's not possible. When linking to a topic you can get the title of the topic to appear by using the <%TARGET_TITLE%> variable. See this topic for details:
http://www.helpandmanual.com/help/index ... erting.htm
(In a related question, is buying v6 still an option? How long will it be supported? I'm also having a lot of trouble with customizing formatting, which I don't remember being necessary at all to output PDF in v6.)
Version 6 is no longer available and you really don't need it. What you describe here has nothing to do with version 7 -- actually, setting up your PDF layouts has become easier since version 6, not harder. If you didn't have to do any PDF formatting before it just means that someone had already set up your print manual template for you.