You have to modify your branch that you created the pull request from.
There are a number of ways to resolve the conflicts.
Assuming your project is using the normal arrangement, a public 'central' repository on github, each developer having a public fork on github, and you having a local clone on your own computer, then the following is the normal way to resolve the conflict.
Pull changes from the central repo into your local clone. There will be conflicts here and git will tell you to resolve them and then commit. You'll have to edit the conflicted source files, use git add
to tell git that you've edited the file to resolve the conflict, and then git commit
to finalize the merge.
During the step where you edit the files to resolve the conflict, you can either manually open and edit the conflicted files (git will insert the traditional conflict markers along with with both sides of the conflict), or you can use the git mergetool
command, if it's configured, to use an external tool to resolve the conflicts. Using mergetool will automatically iterate through all the conflicted files, and also save you the git add
step.
After you've completed the merge locally, you push your changes up to your github fork, updating the branch you based your pull request on, and the pull request is automatically updated. Github should show that the conflicts on your pull request are resolved.