Let me explain how thirty bees installation works:
first, php files must make it into destination directory.
This can be done either by extracting thirtybees.zip file and uploading its content via ftp. This is the most common case.
Alternatively, this process can be automated by some third party tool (softacoulous, etc)
once php files are in destination directory, you just navigate to this directory using your browser, and start the installation process
installer only creates and populates database tables
done
Now, as you can see, during installation the responsibility of this *crap* software is only to populate tables.
If you complain about your root directory being overwritten, then this must have happened during step #1. Depending on what installing option you chosed, there are only two conclusions:
if you uploaded content of zip file via ftp, then you must have fucked up, and uploaded to wrong destination. This is entirely your fault
if you used third party tool (softacoulous, etc), then this third party tool fucked up. And I repeat - third party tool. Not created or maintained by thirtybees.