One inside the DAC, the other inside the scanner. They're how you connect the two. Neither one just comes with a printer-style connector, so in order to use a printer cable you have to provide connectors for it in the DAC and scanner. Otherwise, what will you connect to? If there is no connector, you cannot connect. It's like trying to plug something into the wall where there's no outlet. You have to have a connector (outlet) to plug into. The reason we use a printer style cable is to maintain compatibility with the ILDA (International Laser Display Association) standards. This means that later if you decide to upgrade to a better DAC, you don't have to redo all the wiring.
Maybe you're not yet understanding just what the breakout boards are. You have two options for providing a printer-style connector in the DAC and scanner: You can go to Radio Shack and buy two blank DB-25 (printer) connectors with 25 pins. Then you can solder each connection directly to each pin based on the ILDA wiring standard diagram (can be found through google). That's the hard way. The breakout boards are just a simpler, easier way to wire up a DB-25 connector. That's all. They have no other function than this. They do not process data, they do not control any scanner parts. The merely provide a DB-25 connector that is already clearly labeled with each connection. If you look at the pictures of the breakout board closely you can see these connections and their labels.
Building scanners is not something that is easily done if you have no experience with electronics. I would HIGHLY recommend carefully reading ALL of the main scanner threads here and on PL again. Also, find a basic text on electronic theory from your local library.