First do the 3D tracking. Then select the comp camera and create a 3D stereo rig. That's all there is to it.
Do you know how to set up a render and use an AE 3D stereo rig? It's not as straight forward as you may think. There are dozens of options.
As Rick said, they are two completely independent steps and if you want to get truly a 3D illusion, you have a lot of otehr work to do. You conventional fooatge will never look 3D without separating out the left eye/ right eye stuff.
Individually there are no issues with this technique but if I create my 3D camera tracking, some text and then right click the 3D tracker camera and then click ‘create stereo 3D rig’ it will first say it going has to make it a 2 node camera and when I click ok the text is no longer tracked to the scene, in fact it appears to be flying around almost randomly.