I use "git" user to connect to the repository. I've changed the SSH2 home to /home/git/.ssh (Preferences->General->Network Connections->SSH) and added "id_dsa" file. Unfortunately when trying to connect I receive the following error:
ssh://git@<host>/some/path/Project: java.io.FileNotFoundException: /home/<MY_HOME>/.ssh/id_dsa (No such file or directory)
form CLI it works fine. for EGit I've found a workaround(but not a very convenient one)
if I copy "id_dsa" from git/.ssh to <MY_HOME>/.ssh it works ;/
In Window -> Preferences -> General -> Network -> SSH you can configure the directory where EGit/Eclipse looks for the SSH keys. But why do you create a local user git to access the repository? You only need that user on the server where the repositories are stored. Then you simply save the private SSH keys, which have the rights to sign in with the git user, in the .ssh folder of your user account.