This is how it works:
The hand control applies pressure to both front wheel calipers and one rear wheel (trailing) caliper equally as there is no proportioning valve like a car. There is no caliper on the left rear wheel on any cat utility model.
The foot brake operates only the front (lead) caliper on the right rear. This is on 2006 and older two right rear caliper models. This is referred to as the auxilliary brake in the parts breakdown.
2003 and older have a mechanical foot brake so this does not apply.
2007 and up only have one ( trailing) caliper on the right rear but it still works the same, as the foot pedal has its own master cylinder with a brake line going directly to the same (trailing) caliper.
There are models in 2008 and later that have the single caliper in the leading position on the right rear. It operates the same however.
The foot operated master cylinder has its own reservoir under the seat and the hand control has its reservoir on the hand lever.
When you apply the foot brake it will lock up both rear tires as the diff is locked side to side.
On the older system (2caliper rear) the foot pedal has been known to not work very well but with a new master and new fluid it should work like new.
On the newer system(1 caliper rear) the brake line from the handle bar control lever (master cyl.) and the brake line from the foot pedal master cylinder are both connected to the one rear caliper.
So long story short when you use the handle bar lever you get all wheel braking. When you use the foot pedal you get two wheel rear braking.