You have a sample in the tutorial step 9 that show how to create a slave site into a sub-directory.
If you have the symbolic link allowed (see tutorial step 4 to 7), you can just put the 3 parameters as given in tutorial step 9.
Here it is again the 3 parameters:
Sample values:
* Site ID = slave1
* Domain name = {site_url}/multisites/{site_id}
* Deploy directory = {site_dir}
This will create a slave site into
www.master.com/multisites/slave1
When you will be able to do that you could try change the parameters to do other configuration
Other sample:
* Site ID = slave1
* Domain name = {site_url}/{site_id}
* Deploy directory = {root}/{site_id}
* Create directory = YES
If you want to replicate a website you must use a more sofisticated processing that consist in using the JMS template like shown in the video of tutorial step 13.