Bettysue,
I have a question, is the site that you are making suposed to only be a zen cart so that the ZC is in the root dir or is it a section of the site?
the reason that I ask is aloot of the regular expressions used in the config file are to make your template that is designed for links that notmal go to pages of the same level to go to links one folder level back.

In the brief instructions it says to put the full path to my template in the embed_config.php in the common folder. But how does the html template know where any of the embed files are and visa versa?
how does thos work you ask.
well it takes the file that you have poitned to and reads it in to thme memory.
then it goes through and loks for various patterns like the <body> tag, the <! START/STOP EMBED --> comments, or thins like doc type and strips them or modify them to work w/ the new directory.
it them looks for paqterns to splith the one big html template in to 4 separate varibles,
  1. the head information like javescript and style sheet links.
  2. stuff that goes in to the body tag like onload commands.
  3. body Mark up that goes before the zen cart
  4. body mark up that goes after the zen cart

then it just echos the varibles in the aproprate places.
It knows where the embeded files (I am assuming that you mena like incase and styles sheets, and moyby flash links) are becasue you put them in that template file.
please include a link tp ypu site nad of you would a link to the raw template file in your next post.
JOsh