When applying a patch is there any way to resolve conflicts?

To generate your patch do the following:

git format-patch --stdout first_commit^..last_commit > changes.patch

Now when you are ready to apply the patches:

git am -3 < changes.patch

the -3 will do a three-way merge if there are conflicts. At this point you can do a git mergetool if you want to go to a gui or just manually merge the files using vim (the standard <<<<<<, ||||||, >>>>>> conflict resolution).