You can start Anatomist with a customized configuration even if you share the same user with other people. To use a particular profile, start Anatomist with a profile name (even if it doesn't exists yet). For example :
anatomist -u toto
and then save preferences to keep them for a further session.
Every profile has its own configuration directory, which is localized according to the system (user is the login used to connect to the computer, it can be for example your name):
Under Linux :
/home/user/.anatomist-toto
Under Windows :
C:\Documents and Settings\user\.anatomist-toto\
To start Anatomist with this profile :
anatomist -u toto