BeyondCompare is a very convenient way to merge changes.
What I do is place all my hacked files into a separate directory on my PC, with the same directory structure as the UBB.threads release .tar.gz (or .zip).
When a new version of threads is released, I copy my hack directory, then use BeyondCompare to merge the changes into the hack directory.
I upload the released UBB.threads files to the server, and then upload the hacked files.
Or were you thinking of a different approach?