usr-merge is actually very simple. If you bootup 5.5.1, you will see that now /bin, /sbin, /lib and /usr/sbin are all symlinks. All the files have got consolidated into /usr/lib and /usr/bin
Everything should just work as before, but there have been some issues when updating from the non-usr-merge save-folder. At the update, everything got moved into /usr/lib and /usr/bin, and a couple of things went wrong.