This guide was helpful for me
http://wiki.eclipse.org/EGit/User_Guide#Resolving_a_merge_conflict.
UPDATED
Just a note on that about my procedure, this is how I proceed:
- Commit My change
- Fetch (Syncrhonize workspace)
- Pull
- Manage Conflicts with Merge Tool (Team->Merge Tool) and Save
- Add each file to stage (Team -> Add to index)
- Now the Commit Message in the Stage window is prefilled with "Merged XXX". You can leave as it is or change the commit message
- Commit and Push
It is dangerous in some cases but it is very usefull to avoid to use external tool like Git Extension or Source Tree