Dave P
Thorn have a lot to say on the topic of tandem braking, so have a read when you have (a lot of) time on your hands. Your brake set-up is one that I would be very happy with. Using the rear disc brake for most of your braking is the best way of making your rims last a long time, and tandems have enough weight on the back wheel to make a rear brake a good stopper on flat roads or gentle hills. So, as you suggest, save the rim brakes for serious braking on steep descents or when you have to slow down fast.
With your set-up you have three brakes to share the job on long, steep hills. The first way of avoiding excessive heat build-up is to avoid unnecessary braking. So when it is safe to go fast, do so.
The second way is to brake hard at the last moment rather than gradual braking. This applies on the hairpin roads you get in the Alps.
But on twisty, steep descents you obviously cannot let speed build up, so you should alternate between the brakes, allowing each to have periods of rest. The worst one to overheat is your front rim brake. Use it hard when you use it, but allow it to rest and cool as much as possible. Overheated wheel rims cause inner tubes to blow.
If you are uncertain, pull over and check the rims. If you can keep hold of them there is nothing to worry about. If they are too hot to hold, take a break. Let them cool. In practice few hills will require this, so be willing to do it when you feel the need.
Thorn say that front disc brakes on tandems require forks so beefy that they give poor ride quality. Others may disagree.
