I found a reference to xcloner in a previous post but whether it can be used to do backups wasn't resolved. I've always used xcloner on standard sites, at the click of a button it makes a tar file of the folders and database.

Im a bit scared about trying it incase it messes up my project!

I asked the owner of xcloner and got this reply..

Hi there! Yes, XCloner is compatible with the multisites component,
however on restore, you might need to manually adjust the main Joomla
config file as from what i remember the multisites component alters
that! Other than this, you will be able to restore the site files and
database without issues

Regards, Ovidiu

Ive just tested it on the master site and it seems to have backed everything inc. slaves up in one go. So I'm happy knowing Ive got a backup just incase, ill worry about restoring and the config file if anything were to happen.

If the info that they mention concerning the "configuration" file consists in the patch that is installed in for the "master" website configuration file, this is NOT a problem and the patch can be either restore when you go in the global configuration and Open / resave the configuration.
In this case the wrapper is automatically added when not present.
This is also the case when you go in JMS "check patches" that will detect this case and will add it.

So you can try to restore you website and vierify that this is the only element not correctly restored by xCloner.
This just means that xCloner does not restore the configuration.php files as it was but rebuild a new one.

I suppose the xCloner rebuild the "configuration.php" file to change some values.
Becarefull that with JMS, you have as many "configuration.php" as you have websites.
So it is probable that the other slave "configuration.php" files are not touched and just be saved by xCloner.