For details about the actual parameters to bakonf, see its manpage.
To use bakonf, choose to either:
run it manually, when you want, either always with -L0 or with a combination: weekly with -L0, daily with -L1
use the provided cron script to run it automatically, or create your own
In any case, you have to do something with the generated archives. Write the to floppy, tape, CD, other machine, but don't just ignore them, you defeat the purpose of bakonf.
In this case, just make sure you have the bakonf-generated archive near the date in the past you are interested in. If so:
if your system uses packages/ports, compare the actual package list with the one recorded by bakonf when it created the archive
install/remove software as needed
copy the configuration files for the services you want to rollback over the current files
If you had a catastrophical failure, you should follow these steps:
Reinstall the operating system on a clean machine. Use the given information in the /metadata directory in the archive to achieve an as close as possible configuration as the old system (e.g. partition layout, packages installed, etc.)
Copy all the files in the archive in the filesystem, overwriting the defaults from the packages.