WordPress -> subfolder + sibling folder access

I have a situation where I have several folders that need to live in my public web folder. I need to be able to access wordpress at the site root, so http://mydomain.tld/ will execute index.php within the subfolder /wordpress/, however similarly I need to be able to access files within other sibling subfolders such as /customers/ such that http://mydomain.tld/customers will list the contents of said folder.

I believe that all of this can easily be done via .htaccess, particularly by placing a .htaccess with an allow all within each sibling subfolder, but I wanted to perform a sanity check here first as to the "best" way to accomplish this.

Additionally, I've been having a problem where wordpress is not working within a subfolder. I have followed the example in the Codex at http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory within the "Pointing your home site's URL to a subdirectory" section, however even after having done this, I still get a 404 for wp-admin and so forth, yet root pages load up just fine (ie, http://mydomain.tld/ loads up the default WordPress contents, but http://mydomain.tld/wp-login.php returns 404).

Finally, I want to be sure that .htaccess not only takes into account the potential www, but also direct and other miscellaneous subdomains since I operate with CloudFlare on this server.

What steps should I take to make this work as outlined properly?