I am using the way that the subsite is sharing the same directory with the master site.
After I config a subsite in JMS, it says,
The site 'subsite1' is deployed.
- You can now map your new domain (subsite.xxxx.net) to the directory
'/home/yyyy/public_html/mastersite/multisites/subsite1'.

I got the subdomain configured in the cpanel as well. (use '/home/yyyy/public_html/mastersite/multisites/subsite1' as the documentroot of the subsite)

But when I go to subsite.xxxx.net to try to install a fresh subsite, the following error message is shown.

Forbidden

You don't have permission to access / on this server.

Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.

I then added .htacess to the document root with the content of the following.


Now I could go to subsite.xxxx.net without an error. But instead of a fresh joomla installation of the subsite, it lists the file and directory, which is the following.

Index of /
cache/
config_multisites.php

Finally, I use '/home/yyyy/public_html/mastersite/' (the document root of the master site) as the document root of the subsite (instead of '/home/yyyy/public_html/mastersite/multisites/subsite1'), I could go to the installation page!

So we are supposed to use the document root of the master site as the document root of the slave site under this situation, is it right?
Thanks!

Yes and no.
When you map (assign) the slave site "document root" directory = the master directory than you are using the "antical" method available in JMS 1.0.x.

With JMS 1.1.x or higher, when you are using the Symbolic Link your are simulating this case where you have the same directory that the master/ The difference is that you can not have different "root" slave site and therefore have specific images and templates folder.

So you right to share the same PHP code than the master.
But you wrong if you want to be able customize some direcrtories like the images and templates folders.