Jfarwell,
If you have not spec'ed your frame, I would consider a rear disc brake mount in addition to your caliper brake mount. That option will allow you the ability to change to what ever size wheels you want later. The front fork can also be easily change as needed.
I prefer disc brakes - better stopping power especially for hills and wet weather, and no overheating rims. But, there is a weight penalty. No big deal on a touring tandem. Starting out, we loved our 26 in wheels. We have since went through a set of light 700c and now ride mostly on a set of 29'er. Nice to have the ability to change our mind.
CJ