I've ridden a normal bike that had exposed inners on the right-hand side of the top tube - it was unpleasant to ride because my inside-right knee touched the wire a lot.
I'd suggest running the rear rim brake along the top tube, you can choose to run it on the top or underneath. At the front and rear ends of each section of top tube you could either:
- have a stop brazed on then run a length of exposed inner, then run a short segment of outer around the captain's seatpost to another stop, and a second run of bare inner.
- Run a single housing all the way along the same path, using cable holders either brazed to the frame, or bolted around the top tube.
Don't simply drag the exposed inner cable on your frame - its a steel wire and will quickly erode your paint, and then start cutting into the steel frame. The wire will suffer too, and you don't want to loose half your braking on a fully loaded tandem !!
Which leads to - If you're thinking of symmetry expect to install two sets of brake stops. It is quite normal for a tandem to have two independent separate rear brakes, a disk or rim, and a separate drum brake in the rear wheel. These require two different activation cables, unless you choose to give the drum brake to the stoker.
For the front and rear mechs, I'd suggest down the down tube, under the front BB, and along the keel, then under the second BB. From there it would be just like a normal diamond-frame bike.
When I rode mine, one of the missing things was a Visual Gear Display (shimano's fancy jargon was VGD) to show what gear you're in. There's no easy way for the captain to look at their feet to see the chainrings, and the cassette is twice as far away as normal. So, an inline gauge/readout works nicely.
If you're feeling flush, I think that tandems would be a fantastic place for DI2 wireless to be used. The captain and stoker could have their own set of gear-buttons each, and have some shared level of control for the gear setting. But this isn't a cheap way to go, however it does avoid two gear cables, at the cost of carrying around some small batteries on each mech. Food for thought in the future perhaps. And you can both have a Di2 readout displaying the current gear setting.