Nubuilder is a combination of PHP files (in the productionnu2 directory) and a mysql database (which contains some zzsys tables that are needed by nubuilder)
Nubuilder cannot start with a totally blank database - one with no tables. The downloads currently come with 2 databases - sample, and samplenufinancial
The sample database/site is as close to "blank" as nuBuilder gets - this is the starting place
The SampleNufinancial database/site is the beginings of an invoicing system - to demonstrate one of the infinite number of paths you could take nuBuilder down...
I hope this helps answer your question - let us know if you are still lost.
This link is still broken - it would be nice to have a known working "starter database" that has everything that nuBuilder needs to work, but no "dummy" data or extra information that simply isn't needed.