Hi Edwin,
thanks for the reply.
I did as you suggested. but I get the following error...
* JFolder::create: Could not create directory
* The deployed directory [/var/www/html/one] does not exists.
So... I started again.
One a fresh server build, whenever I install the "slave1" site (called bdomainb), it creates the "multisites" folder no matter what I do. 
So I always get /var/www/html/multisites/bdomainb. 
It seems to be hardcoded in there somewhere.
So what I did was MOVE the bdomainb subdir one subdir up to the same level as "multisites". Like this... /var/www/html/bdomainb.
Then I created the template and the sites called One and Two. However they both point back to bdomainb.com
Such that...
www.bdomainb.com      I edit this and it changes
www.bdomainb.com/one    to exactly the same and 
www.bdomainb.com/two    is exactly the same as bdomainb.com. The template etc are all changed at the same time no matter what I do. It seems they all just point back to 
www.bdomainb.com.
So no matter what I do I only seem to have one site. It should be three seperate sites.
DNS points to the sites ok.
Current config below. Any cluesticks as to what I'm doing wrong please?
Thanks,
Bendo.
root site	
Database type = mysql
	Host name	= localhost
	Database name = db1_
	Advanced/ Table Prefix/ = jos_
/var/www/html/bdomainb/	
site ID = 	bdomainb
	list of domain names = 	
www.bdomainb.com
	template = 	Fresh slave site
	master site directory = /var/www/html
	deployed directory = 	/var/www/html/bdomainb
virtuemart template	
ID =	virtuemart
	list of domain names = 	http://{site_url}/{site_id}
	New DB prefix = vm{site_id}_
	master site folder = /var/www/html
	Deployment folder = {root}/bdomainb/{site_id}
var/www/html/bdomainb/one	
site ID = 	one
	list of domain names = 	
www.bdomainb.com/one
	template = 	virtuemart
	new site title = 	One
	deployed directory = 	/var/www/html/bdomainb/one
var/www/html/bdomainb/two	
site ID = 	two
	list of domain names = 	http://{site_url}/{site_id}
	template = 	virtuemart
	new site title = 	Two
	deployed directory = 	/var/www/html/bdomainb/two