If this is a book, you may not need to unlink the sections. If the text
that is to be different is something in the text itself (such as a chapter
title), you can use a StyleRef field to pick it up. You will probably still
want to have section breaks (Next Page or Odd Page) between chapters so that
you can use "Different first page" to omit a header on the first page of a
chapter, but using StyleRef keeps you from having to manually enter the text
in each header (and allows you to leave them linked, as well).
Book layout can vary considerably, but what I usually do, just for
simplicity, is use a centered drop folio (page number in the footer) on
every page. The First Page Header is blank, and the Even Page Header and Odd
Page Header have Book Title and Chapter Title (if any) or Book Title and
Author Name, also centered. In one book that was a collection of letters (no
chapter titles), I used a StyleRef field to pick up the date of the first
letter on the page.
Occasionally I'll put page numbers in the headers (outside) with the running
heads aligned to the inside, or I might align the running heads to the
outside and have the page number, also Outside, in the footer. It just
depends on the book. Note that if you choose Outside alignment for page
numbers in the footer, then you need to make all chapter starts either even
or odd so that you can replicate the Outside placement of the page number in
the First Page Footer.
As for templates, have you looked at
http://word.mvps.org/FAQs/Customization/CreateATemplatePart2.htm?