Genealogy programs normally save genealogy data into their own database, one that can only be read by their own program and maybe a few utility programs specifically written for it.
Version 1.0 of Behold doesn't work that way. Currently Behold loads its data into memory. Internally it uses an extended version of the GEDCOM format to allow it to understand genealogy data from just about any source. Version 1.1 will be different, and Behold will then write its data to disk, which will be called project files. This will be the needed first step that will allow saving your data and editing in Version 2.0.
Behold's Behold Organize files that it saves do not contain genealogy data. They only contain instructions on how to open and organize other genealogy data files, currently just GEDCOM files. Soon, by Version 2.0, Behold Organize files will be able to manipulate Behold's project files as well.