Answer to first question, Instructions for using RAT.
1. download and install java if necessary http://java.sun.com
2. download the current RAT jar from http://code.google.com/p/arat/ [rat-0.5.1.jar]
3. from the command line, execute the jar file [java -jar <path-to-rat.jar> <path-to-source-tree>].
As for the second question, I found the following [from http://www.apache.org/legal/src-headers.html]
What if my project includes its web site within a product distribution?
With few exceptions, all human-readable Apache-developed files that are included within a distribution must include the header text. Documentation, including web site documentation distributed with the release, may include the header text within some form of metadata (such as HTML comments) or as a header or footer appearing in the visible documentation.
What files in an Apache release do not require a license header?
A file without any degree of creativity in either its literal elements or its structure is not protected by copyright law; therefore, such a file does not require a license header. If in doubt about the extent of the file's creativity, add the license header to the file.
I also found some discussion http://www.nabble.com/Rat-tool%2C-Apache-header-and-different-file-types-tf2352902.html#a6553062 that seems to indicate that the documentation should have the ASL header in there.