Every object in PDP++ can be saved to a file, and loaded back in later from that file (see section 8.1.3 Saving and Loading Objects). Typically, a user will simply save and load the project object, since it contains all the other objects of interest, which will be saved and loaded along with it. However, it is often a good idea to save parts of the project, particularly environments, since that makes it possible to load these parts into other projects.
A saved project file is actually human readable (once it is uncompressed), and you can pull it up in your favorite text editor (if its not too big for it), and see exactly what parameters were used, etc. This is much easier to do if you just save all of your specs, which contain most of the interesting parameters in the project. Thus, saved files serve as records of exactly how your simulation was configured.