As Rick states, the camera is aware of the presence of the TC, and even records it in the EXIF data. I think the 70-200mm f/2.8L IS II does pretty well with teleconverters. Here are links to three examples:
Note that the two shots with the 7D are both at ISO 3200, which is pretty noisy, and the first shot was shot in heavy mist/drizzle (which is why I was using the 70-200+TC instead of the 100-400, since the latter is not weather sealed.

Back to the point at hand, the EXIF for the middle shot, for example, shows the lens as "EF70-200mm f/2.8L IS II USM +2.0x" and the focal length as 400mm.

So, you have to calibrate each lens and lens + TC combination separately, and each combo counts against your max of 20 stored adjustments.

FWIW, the 1D X will go a step further and actually associate adjustments with the serial numbers of the lens and/or teleconverter - useful for studios with multiple copies of lenses that require differnet adjustments, since other cameras wouldn't know my 70-200mm f/2.8 IS II from Rick's copy of the lens, and so would apply the set adjustment to any lens of that type.

While I think the 70-200 II plus TCs delivers usable images, I was less pleased with the 100-400 + TCs, it just doesn't stand up to them that well (and as Pat states, unless you nave a 1D III, 1Ds III, or 1D IV, you can't AF with the 100-400 + 1.4x anyway, fo FoCal wouldn't be of any use...