Your easiest solution here is to keep everything in your cms folder.
and follow this step found at
http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory
This will keep all wordpress related files in the cms folder, but it will look like its running from the root, copy of index and some .htaccess wizardly as you call it :).
enjoy
Using a pre-existing subdirectory install
If you
already have WordPress installed in its own folder (i.e.
http://example.com/wordpress) then the steps are as follows:Go to the Generalpanel. In the box for Site
address (URL): change the address to the root directory’s URL.
Example: http://example.comClick Save
Changes. (Do not worry about the error message and do not try to
see your blog at this point! You will probably get a message about
file not found.)Copy (NOT MOVE!) the index.php and
.htaccess files from the WordPress directory into the root
directory of your site (Blog address). The .htaccess file is
invisible, so you may have to set your FTP client to show hidden
files. If you are not using pretty permalinks, then you may not
have a .htaccess file. If you are running WordPress on
a Windows (IIS) server and are using pretty permalinks, you’ll
have a web.config rather than a .htaccess file in
your WordPress directory. As stated above, copy (don’t move) the
index.php file to your root directory, but MOVE (DON’T COPY)
the web.config file to your root directory.Open your root directory’s index.php file in a text editor Change the following and save the file. Change the line that
says:
require(‘./wp-blog-header.php’);
to the
following, using your directory name for the WordPress core
files:
require(‘./wordpress/wp-blog-header.php’);Login to your site. It should still be
http://example.com/wordpress/wp-admin/If you have
set up Permalinks, go to the Permalinks panel and update your
Permalink structure. WordPress will automatically update your
.htaccess file if it has the appropriate file permissions. If
WordPress can’t write to your .htaccess file, it will display
the new rewrite rules to you, which you should manually copy into your
.htaccess file (in the same directory as the main
index.php file.)