I've watched the tutorials, and I've read the document, and I cannot get my sites to have unique folders for 'images' and 'templates'. I just don't get how these templates work.

At the moment I have two slave sites on the same database with different prefixes. I do not have a site template created, as I don't understand their usage here. I don't want to have any front end editing, only control over the sites myself. How do I manage to separate the installs so they have custom image and template folders? I have the content separate, just not the folders.

Thank you for making a much needed extension (works great, and I know it does what I need just can't get it configured!),
Jeremy

When you create a slave site, you can specify the image and folder directory that is relative to your "hosting server" directory path (normally the deployed directory).
The image and media folder is a standard Joomla parameter that can be configured in Joomla Global Configuration.
JMS just give the opportunity to fill those parameter (that are stored in DB) when you replicate the website from a "website template".

Therefore, when the slave site is already created you can update the image and media folder directly in the Joomla Global Setting.

The "Website Template" is used to define the rule of the replication.
It is mainly used when you have several slave site to create based on the same website.
In JMS, you can define a generic rule in the "Website Template" that can be resolved when the website will be created based on this "websitie template".

In general, you specifcy a deploy dir (ie. {site_dir} and you can use the medi and image folder as usual (images and images/stories).
You have to fill those field to make them specific. Otherwise it will create a link to the master website.

However the folders are not being picked up, and I've tried just about every combination of configurations. The template one finally did get picked up, but then my front end site doesn't return anything, its a blank file. I'm stuck on this one, would providing login information help?

Also I have to CHMOD the slave config file once in a while, somewhere it changes from 644 to 444. It happens when I update the config in the slave site, and then in the master try to change something in multisites.

Send me by email your URL, login and password of your master website and I will have a look tomorrow on your configuration.
I will also need a FTP URL, login and password to let me check the permission of the files and folders