Here's a quick summary of the steps to follow (my second non automatic merge).
git pullThis pulls new updates to your local repo /working directory and notifies you there are conflicts that couldn't be automatically merged.
git mergetoolOpens your favourite $EDITOR with a 3-vertical panel split. Showing you local, merge and remote buffers. Edit the file and clean it.
git add fileWithConflictGit knows what you're trying to do, so it will write the "merged from github...." for you.
git user manual explains how to do it fairly well. Of course, you can search on stackoverflow for user help. Many use rebase to "flatten" the branch history. That's up to you. Myself, I'm not confident enough to use those smart commands (Although git fans say that rebase is a git killer feature).