Motion Studio is either in setup or animate mode. These modes correspond to the main tabs on the interface. When on the Setup tab, Motion Studio is operating in setup mode; when on the Animate tab, Motion Studio is operating in animate mode.
In setup mode, IK and attachments are inactive. Moving a joint in setup mode resizes it's bones instead of moving other joints. Also, moving a joint (or bone) does not affect any attached objects.
Use setup mode to make changes in the way joints are connected or the way bones are attached to objects. And, of course, for a new skeleton, setup mode is used to position joints and bones in the first place!
In animate mode, IK and attachments are active. Moving the joints causes the bones to react with IK, and any attached objects are affected accordingly. This is the normal mode for setting poses and recording keyframes.
When you go to animate mode from setup pose, the pose the skeleton is in becomse the rest pose. The rest pose is then automatically recorded to frames 0 and 1 in trueSpace. When you return to setup mode from animate mode, trueSpace is rewound to frame 0 and the rest pose is restored. Note that you can also change the rest pose from animate mode by recording into frame 0.

When Motion Studio starts, it will enter setup mode if there are no skeletons in the scene; otherwise, it starts in animate mode.