For each conflicted file you get, you can specify
git checkout --ours -- <paths>
# or
git checkout --theirs -- <paths>
From the git checkout docs
git checkout [-f|--ours|--theirs|-m|--conflict=<style>] [<tree-ish>] [--] <paths>...
--ours
--theirs
When checking out paths from the index, check out stage #2 (ours) or #3 (theirs) for unmerged paths.The index may contain unmerged entries because of a previous failed merge. By default, if you try to check out such an entry from the index, the checkout operation will fail and nothing will be checked out. Using
-fwill ignore these unmerged entries. The contents from a specific side of the merge can be checked out of the index by using--oursor--theirs. With-m, changes made to the working tree file can be discarded to re-create the original conflicted merge result.