I'm experiencing the same problem with file/directory permissions with a Joomla 1.5 install.
I installed Joomla1.5 successful and I am able to log into the system. The problem starts when I try to add a template. I get the JFTP::write message. I have traced this to being a permission problem. Therefore I am not sure if I need to move to suphp or if I can stay with the default.
I am able to use the media manager and upload pictures and remove pictures, create articles, etc. The only thing I cannot seem to do at this time is upload a template form a zip file.
The tutorial posted for Joomla/ISPConfig is only for the first version. Any thoughts would be appreciated.