In the documentation under the 'share the whole site' section it says: 'Remark: You can not change the default theme selected in the website but just change the
PHP code relative to this theme.'

I'm unsure what you mean by changing the PHP code relative to the theme. Change what exactly?

Is this question or knowledge? i can't understand what you want to say.

It's a question. I have a slave site setup using the 'Share the whole site:' option. How do I setup a new default theme on the slave that is seperate from the master default theme?

Share a whole website mean that you use the same DB with the same table prefix for the different website.
As this is the same DB for the webiste, this also mean that the default joomla template is the same. You can not change the default template as this is an information that is stored in the DB.

As the joomla templates are saved on the disk into the /templates directory, the only thing that you can do is to put other files into a directory that have a same name.

Ok thanks I understand now.

I can succesfully get slave css edits to appear in a browser. I cannot get slave index.php layout changes to work. The slave site keeps reading the master index.php. How do I change this to get the slave index.php to appear?

On which Joomla version to you edit the index.php present in your master instead of the slave site one ?

Which Joomla template do you use ?
Some of them use a specific framework that replace the standard joomla framework.