Your Atelier server connection information is stored in Eclipse's secure storage file. The secure storage file is shared among different workspaces created in the same Eclipse client. You can see the location of this file in your Eclipse preferences under General > Security > Secure Storage > Contents > Storage location.
The location of the secure storage file depends on the directory in which Eclipse was installed. If you want a second install with an independent list of server connections, you will need to install the second Eclipse client in a new directory.