Moving Drupal from root to subdomain

I have drupal installed as the root of my main domain. But I have now added some subdomain/add-on domains to that account (which do not use the main domain name), and the drupal mods to the .htaccess file makes these subdomains unusable. I have confirmed this by removing the .htaccess file and it works as expected.

I realise that with some tweaking I could probably get these sites to work in harmony, but I dont want to have to edit the .htaccess for each new add-on domain... but I would still like to know how to do it for the interim. Somehow work out what lines are drupal specific and tell them to ignore my add-on domains, or some other way... HELP

What I would really like to do is clean up the root of my public_html folder by shipping my drupal installation to a subdirectory or subdomain of it (either/or).

I know it is not as simple as moving the files from the root of public to a sub folder, what other edits would be needed? ie, obviously some edits to the .htaccess files, but what about db settings? I'm sure from my Drupal 4 days there is a reference to the location in there somewhere 9but that was so long ago)...

Any help appreciated...

Not sure if anyone wants to see this, or needs to, but here is my .htaccess file:

AddHandler application/x-httpd-php5 .php
#
# Apache/PHP/Drupal settings:
#
# Protect files and directories from prying eyes.
<FilesMatch "\.(engine|inc|info|install|module|profile|po|sh|.*sql|theme|tpl(\.php)?|xtmpl)$|^(code-style\.pl|Entries.*|Repository|Root|Tag|Template)$">
Order allow,deny
</FilesMatch>
# Don't show directory listings for URLs which map to a directory.
Options -Indexes
# Follow symbolic links in this directory.
Options +FollowSymLinks
# Customized error messages.
ErrorDocument 404 /index.php
# Set the default handler.
DirectoryIndex index.php
# Override PHP settings. More in sites/default/settings.php
# but the following cannot be changed at runtime.
# PHP 4, Apache 1.
<IfModule mod_php4.c>
</IfModule>
# PHP 4, Apache 2.
<IfModule sapi_apache2.c>
</IfModule>
# PHP 5, Apache 1 and 2.
<IfModule mod_php5.c>
</IfModule>
# Requires mod_expires to be enabled.
<IfModule mod_expires.c>
# Enable expirations.
ExpiresActive On
# Cache all files for 2 weeks after access (A).
ExpiresDefault A1209600
# Do not cache dynamically generated pages.
ExpiresByType text/html A1
</IfModule>
# Various rewrite rules.
<IfModule mod_rewrite.c>
RewriteEngine on
# If your site can be accessed both with and without the 'www.' prefix, you
# can use one of the following settings to redirect users to your preferred
# URL, either WITH or WITHOUT the 'www.' prefix. Choose ONLY one option:
#
# To redirect all users to access the site WITH the 'www.' prefix,
# (http://example.com/... will be redirected to http://www.example.com/...)
# adapt and uncomment the following:
# RewriteCond %{HTTP_HOST} ^example\.com$ [NC]
# RewriteRule ^(.*)$ http://www.example.com/$1 [L,R=301]
#
# To redirect all users to access the site WITHOUT the 'www.' prefix,
# (http://www.example.com/... will be redirected to http://example.com/...)
# adapt and uncomment the following:
# RewriteCond %{HTTP_HOST} ^www\.example\.com$ [NC]
# RewriteRule ^(.*)$ http://example.com/$1 [L,R=301]
# Modify the RewriteBase if you are using Drupal in a subdirectory and
# the rewrite rules are not working properly.
#RewriteBase /drupal
# Rewrite old-style URLs of the form 'node.php?id=x'.
#RewriteCond %{REQUEST_FILENAME} !-f
#RewriteCond %{REQUEST_FILENAME} !-d
#RewriteCond %{QUERY_STRING} ^id=([^&]+)$
#RewriteRule node.php index.php?q=node/view/%1 [L]
# Rewrite old-style URLs of the form 'module.php?mod=x'.
#RewriteCond %{REQUEST_FILENAME} !-f
#RewriteCond %{REQUEST_FILENAME} !-d
#RewriteCond %{QUERY_STRING} ^mod=([^&]+)$
#RewriteRule module.php index.php?q=%1 [L]
# Rewrite current-style URLs of the form 'index.php?q=x'.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
</IfModule>
# $Id: .htaccess,v 1.81.2.3 2007/09/21 12:24:22 drumm Exp $