I have installed MS FTP and a default ftp site exists in IIS.
When i try to logon i get directed to the Inetpub\ftproot folder and cant access the website folder.
There is an ftp user in the domain section but there isnt an ftp site. Just domains?
 
Any help appreciated thanks

Are you using MSFTP 7.x ? if yes then you will need to follow instructions given in this Article to configure it in the HC Panel.

Im not sure about the version of MSFTP im trying to find the number but i spent 2 hours following that article last night trying to to work it out as the instructions bare no resemblence to what is available to me in iis.
 
when i added MSFTP as a service it created the default site.
 
If i try to create another default site i get the isolation option but in no comparison to where the article states that it is so is just coonfusing.
 
without creating my own there is no way i can find to have access to those settings.
 
The article is very unclear also regarding the anonimous connection as it states Allow anonimous connections???
 
I deleted the original and installed a new odefault site and followed the instruction as best as i could as they dont match what actually apens in server 2003. 
 
I now get a 530 error cant connect. And there isnt a choice in HC serrver manager just the default website drop down menu. Nothing else

Im now getting this error:
 
connection attempt failed eai_noname neither nodename

By default MSFTP 7.x comes with Windows 2008 Server and  MSFTP 6  with Windows 2003.
That Kb article include complete instructions to configure the FTP 7 with Hosting Controller, if you still unable to connect it with HC then I will recommend you to contact HC support team by open a trouble ticket and provide them the Server RDP and Panel credentials they will fix the problem for you.