htaccess configuration directories for subdomains and root domain - .htaccess

Question

My folders in my www directory as set up as follows:
www/forums
www/helpdesk
www/www
In the base www folder (not www/www), I have the following set up in my htaccess file to redirect based on subdirectory
# Direct subdomains to appropriate folder in WWW directory
RewriteCond %{HTTP_HOST} ^example\.com$ [NC]
RewriteRule ^(.*)$ http://www.example.com/$1 [L,R=301]
I also have the following set up for configuring the index.php on the main site (www.example.com) - this is also in the htaccess file in the www directory:
# Rewrite rules
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^(.*)$ www/$1 [L,QSA]
The problem I am facing is that I have stuff from forums.example.com that I want to embed in www.example.com (Vanilla Forums + WordPress plugin) - if I configure this using the admin panels, the iFrame gets blocked because they are different domains.
I found out that when I go to www.example.com/forums, I get the same front page as forums.examples.com - but all the clean URLs break.
When I look at the .htaccess file in the www/forums folder, I see the following configuration
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ index.php\?p=$1 [QSA,L]
What do I need to do to the .htaccess file in the www directory so that when I go to www.example.com/forums, it works the same as if I went to forums.example.com

Answer 1

...the following set up in my htaccess file to redirect based on subdirectory
# Direct subdomains to appropriate folder in WWW directory
Aside: That snippet is just a canonical non-www to www redirect. It doesn't "redirect based on subdirectory" nor does it "direct [any] subdomains". (?)
the iFrame gets blocked because they are different domains.
It sounds as if you need to set an Access-Control-Allow-Origin HTTP response header on forums.example.com to allow the content to be "embedded" in example.com? Something like the following (using mod_headers) in the www/forums/.htaccess file:
Header set Access-Control-Allow-Origin "http://example.com"
What do I need to do to the .htaccess file in the www directory so that when I go to www.example.com/forums, it works the same as if I went to forums.example.com.
How do "all the clean URLs break"? However, given the HTTP header mentioned above, you shouldn't have to do anything more and still access forums.example.com (not the subdirectory).
Incidentally, the fact you can access the subdirectory (that the subdomain points to) is just how your hosting is configured. Normally you should block access to the subdirectory in order to prevent duplicate content issues (and any other issues, such as the linking problem you mention).
Also note, that due to the way mod_rewrite directives are inherited (or not in this case). The mod_rewrite directives in the www/forums/.htaccess file completely override the mod_rewrite directives in the parent folder.