I created a custom layout by creating a new templates subfolder and copying the template files I wish to change from the templates/user folder into the new templates subfolder.
 
The layout has been switched over and the new template is starting to look how I want. All except for the site search. Our site search box is in the "header" of our template.
 
What I've done so far is copy the templates/user/block_site_search_form.html to our custom template directory, modified it to fit the look, but nothing shows up when I include the block into the header.html template using {block_site_search_form}
 
I am working with the "home page layout" for now just to get the template working and have added the site_search block to the left column (don't know if there's a better way to make a block available to the template?)
 
Thanks!

Well, I'm not sure if this is right or if there is a better way as this is the first I've worked with this cart, but I have something.
 
In 'header.php' at line 39 above the line reading:
 
$t->set_file("header", "header.html");
 
I added this:
 
include_once("./blocks/block_site_search_form.php");
$t->set_file("site_search_form", "block_site_search_form.html");
$t->parse("site_search_form", false);
 
Then in templates/myLayout/header.html I added
 
{site_search_form}
 
to the location I wanted the customized 'templates/myLayout/block_site_search_form.html' to be displayed.
 
Again, I don't know if this is even close to being proper or if I missed an easier way, but so far this seems to do the trick.

Thanks Elijah, but while the search form now appears where I want, the search part doesn't actually work - just refreshes the current page when I click the "search" button. Any ideas?