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To upgrade from a previous OWTF version please follow these steps (capitals for emphasis, not shouting!):
1) Uncompress new version into a _SEPARATE_ directory
2) Import your settings from PREVIOUS_owtf_dir/profiles/general/default.cfg into NEW_owtf_dir/profiles/general/default.cfg
3) If you changed other owtf_dir/profiles files, you should also import your details as above (otherwise you may miss new OWTF settings)
4) Tool location wise you have two options: Move tools to the new OWTF folder or simply reference their locations in NEW_owtf_dir/profiles/general/default.cfg (maybe easier?)
It might also be useful to create a symbolic link to a well known dictionary and tool directory on your filesystem, for example:
root@bt:~/OWTF_0.11_Vienna# ln -s /root/owtf_dev/tools/ tools
root@bt:~/OWTF_0.11_Vienna# ln -s /root/owtf_dev/dictionaries/ dictionaries
IMPORTANT: When creating symbolic links, be careful not to delete the original directory. Use rm -f instead of "rm -rf" to delete the links!