You/ve picked a very difficult thing to do, albeit, it's something I would like as well. But I think it would require a major change in the way ISPC works to achieve.
So you have to look at workarounds. True you could tell your ftpd to allow root login, but this is extemely dangerous. You're best bet is to research an sftp (scp) method of connecting to the server to provide a form of root access so as to connect to all directories (or at least /var/www). Again this could prove dangerous and it's possible ISPC will not like the owner/perms of the files written to the various web dirs. I don't know what will happen if this is done, but it's also something I plan on looking at in the future as clients with multiple websites cannot understand why they need a different ftp login for each site.
You are lucky that you only have one client on the server.