The 29" designation refers to the outside diameter of a 700c tire that is about 29" (xx-622). The 622 is the rim size. The xx number (width) will be relatively large 60mm+ for a 29" tire. 26" Big Apples in 60-559 (aka 26" x 2.35") have about a 27.5" outside diameter. It's all a little confusing, unfortunately.

Ultimately, you need to match the tire to the rim and to the frame and fork. Also, you need to match the inside diameter of the rim to the tire width. If the tire is too wide for the rim, the rim will fail or the tire will feel squirmy, and if the tire is too narrow for the rim, the tire will not seat properly.