The linked system is discussed in the owners manual.....a little. Basically, applying front brake activates light rear braking. Applying relatively heavy rear brake activates the front brakes on one rotor (the throttle side, I think). So, in a sense you can control the amount of front or rear braking by using one over the other in terms of greater pressure. But I don't think there's any practical difference when riding, and I wish there was a switch available to activate or disable the linked system. I prefer to have control over both brakes independently.
OTOH, the system does a good job of keeping the bike balanced and stable, so I use the pedal the same way I would in a non-linked system, for trail braking on curves. The system applies some braking in front, and the bike rides though the curves beautifully. Around town, I don't even bother using the rear brake.