I can post pictures if it would be helpful, but we've removed the roof rack (too big a mileage hit and noisy) and now haul our tandem inside our Honda Fit (first gen, but should work with all years).
The bike goes from the glove box to the back window and the stoker rides behind the driver in the car. For our tandem (Cannondale RT2000 size L/S, I think), only the front wheels needs to be removed. Others have had to loosen or remove handlebars, rear wheel, etc., but none of that was necessary for us. Loading is actually quite easy as well, but is best done with two people. We also put a sheet down on the seat to keep things clean.
We think this is a great solution and a perfect way to travel with a tandem and still get over 30 mpg! Of course, your mileage may vary!