I run several multi-sites and nothing is being shared between them except core and the modules and themes below
sites/all/. If more than this is shared (your question specifies "everything"), then you've not set up your multi-site right.
I've written a tutorial about setting up a multi-site here. I hope the instructions are clear enough to follow.
Setting up a multi-site where the primary site is in a sub-directory is not different from setting up any other multi-site, provided your
DocumentRoot points to the right place.
From your latest comment, I finally understand that you're trying to do the same thing as the person at http://drupal.org/node/1882182.
In that case, you need to understand that this person is not using the subdirectory method. He is using the subdomain method. You can't mix these methods, you must use one or the other.
And if you're using the subdomain method, you must not use a symbolic link (as you indicate in your question that you're using). Instead, you must configure DNS and your vhost to point to the directory that is your
DocumentRoot for Drupal (in your case, it sounds as this should be
/var/www/html/sub1/. This will take care of the fact that your Drupal core is installed in a sub-directory with a plain HTML-site in the web-root. You must also create the following sub-directory in the Drupal
sub2.mysite.com. Copy the
sub2.mysite.com. Then make
sub2.mysite.com your working directory and immediately copy
settings.php. Make sure that both are writeable by the web server user. The
sub2.mysite.com subdirectory will hold your
sub2.mysite.com. Then go to your ISPs control panel and configure DNS for
sub2.mysite.com to resolve to your main site's IP-adress. Finally create the following ServerAlias:
ServerAlias sub2.mysite.com in your main site's vhost configuration file.
You should now be able to point your web-browser to
http://sub2.mysite.com/ and be greeted with default Drupal installaton screen. You can then proceed and install the multi-site instance you've created. If you get anything else than the default Drupal installaton screen at this point, something has gone wrong and you need to find out what this is.
(All this assumes you're using Apache2 as your web-server. If you're using something else, you need to figure out the equivalent of
ServerAlias on your brand of web-server.)