I wouldn't advise putting your HTML files on a Samba share that is also the directory for your website.
If someone hacks the webserver, your original files could be gone! The best recovery from a hack is a complete rebuild of the system, with the latest patches, so unless you have backups you may be playing with fire.
Your method does make some parts of management easier though. If you can afford it, it's best to have your webserver totally dedicated to serving pages.
I put my pages in a user (/home) subdirectory on a dedicated server and point Apache to that subdirectory. I FTP/SCP the files to the directory as that user and my permissions work just fine.
This method, though more cumbersome, provides better file protection.
Hope this helps.