For all those who cannot apply the patch with the three-way merge, I have found a good solution under this link that works for me: git.vger.kernel.narkive.com

I did the following steps from the answer:

1. Run git-am to get the number of the failing patch
2. Apply the patch manually, but turn on verbose and reject in git-apply
   git-apply --verbose --reject changes.patch
   Then the conflicting file(s) will be saved as <filename>.<extension>.rej
3. Manually resolve the conflicts

Please check the link for the original, more elaborate answer.