There will never be a “merge” facility developed in kiwitrees. It is simply not practical. For more information about this see: http://kiwitrees.net/?p=4267
But you do have existing features that can be easily used for what you describe.
1 – Append family tree. Use this to combine your two trees into one single tree.
2 – Find duplicates. Use this to find the likely duplicates in your new tree.
3 – Merge duplicates (directly linked to “Find duplicates”) to merge each duplicate into a single record.