How to NOT share content between multi sites? Try as I might cannot stop all changes in one sub site copying to other. They have two separate databases and settings files and conf files but because of necessary symlink to share core code base , everything else is being shared right along with it.

How can I stop this sharing everything between subsites when drupal core is in first subsite and symlinked to second?

Why is it even happening when have two sep db set up and two sep settings.php?

I don't want changes to be made to subsite2 when I make changes to subsite1 and vice versa as is happening now.

mysite.com (static html) in /var/www/html

sub1.mysite.com  (drupal install) pointing to mysite.com/sub1 

/var/www/html/sub1/sites/sub2

sub2.mysite.com (symlink to sub1 in html folder) pointing to mysite.com/sub2(symlink vs)

No necessity to add sites.php or even change httpd or conf file with symlink.

My theory is you must have drupal core files in html folder not a subdir linked to subdomain below it. I will test tomorrow.

No I think I need to just know what to put as base url in conf file? Do I direct it to html/mysub.site.com  or to html/sub1/sites/mysub.site.com ?
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 sites directory: sub2.mysite.com.  Copy the default.settings.php into sub2.mysite.com. Then make sub2.mysite.com your working directory and immediately copy default.settings.php to settings.php.  Make sure that both are writeable by the web server user.  The sub2.mysite.com subdirectory will hold your settings.phpfor 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 DoccumentRoot and ServerAlias on your brand of web-server.)