There are several questions.
Before replying to the other question that would be more easier for you to discover if you have the slave site working, we first have to check how you have setup the slave site
Have you followed the tutorial and the different steps.
It show how to install JMS, how to check the environment and how to check the creation of a slave site.
In your question, we don't have provided any technical information to know your environment that correspond to video 3 to 7.
Are you using a Unix platform or Windows platform ?
Do you have symbolic link available or not ?
When you say that index.php is empty perhaps this is a Symbolic Link that does not seems correct.
Normally the index.php must call the content of the joomla original index file.
So the first element is to check your environment.
Perhaps you can also check the permission of the directory and try understand why you have an "empty" index.php file.
In the video presented in the tutorial (that depends on your environment), when you have symbolic link, you can see the result expected.
Once you have identified the probably permission issue, then you can effectivelly create quickly your 25 websites based on JMS templates rule that you have to define.
If you want to share some extension, see the tutorial video 16
www.jms2win.com/tutorial#jms12x-16