I have a server running postfix and dovecot with several email accounts. Is it possible to install ISPConfig 3 on top of it or is the configuration going to erase the accounts? Do I have to backup the email accounts and move them back after the ISPConfig Install or can I somehow add the accounts to the ISPConfig configuration?
No. Look at the ISPConfig installation guides. They all start with an empty host. If the host allready is running something, do not try installing ISPConfig.