Hi Sersh,
you are right that the install for the first domain is in the index directory. But I will get the problem within update the second (all in ftt directory) installation but with file permission problem from first one.
It seems to me that the auto-update will control every installation on the server as well for all installation which are up-to-date. Maybe it is better to update each one instead of single installation.
Right now I will change the permissions before updating - that not so a big problem
thx alex