There are a couple of options to use LCMS for your entire website. If you place it in root, the root files get cluttered with your own files and the LCMS files. Further it may make it more difficult ot manage in future cases of LCMS updates. Finally, LCMS references a few ../ files. So if you place it in your domain's root, your CSS files may not work.
To resolve all of the issues I place LCMS in its own directory /lcms. Then I copy the original .htaccess file that comes with LCMS to my domain's root. I make the following modifications:
Changed line:
RewriteRule ^(.*)$ public.php?-path=$1
To now be:
RewriteRule ^(.*)$ /lcms/public.php?-path=$1
Changed line:
RewriteRule ^/(.*) https://%{SERVER_NAME}/$1 [L,R]
To now be:
#RewriteRule ^/(.*) https://%{SERVER_NAME}/$1 [L,R]
RewriteRule ^(.*) /lcms/admin.php
Obvioulsy this is just a simple commenting out then adding my own line. I am not sure if this will cause any security or other issues. Hopefully Mr. Steve will be able to comment on them as he has time.
While my site can be served from LCMS now, I still have an issue of the CSS not working from pages that use the include public.php method.
More to follow if I figure it out.