Beyond compare is not so tough to use at all. I did it like this.
I have a [UBB 6.04f] folder where I keep a local copy of the older Ubb on my hard disk. It looks exactly like when you unzip the zip file for your ubb and all the modifications have been done there.
Then I unzipped the updated ubb into another folder [UBB 6.05]. When using Beyond Compare, simply set the two directory to the older UBB [UBB 6.04f] and the newer UBB [UBB 6.05]. The program will compare all the files in the two folders and show you which file and portion is different. Synchronising the different files is done with just one button. Upload the new UBB files and you're done.
I hope this helped someone. Cheers.