You can use the Translate, Rotate, Twist, and Scale tools to align sections of the bone system to the figure you are creating/editing. The following rules apply:

• Clicking in the middle of a bone allows the selected tool to modify both the selected bone and its children, including joint settings and spherical falloff zones.
• Clicking near the beginning or end of a bone allows you to move just the selected endpoint. Directly editing bone origins and endpoints does not affect spherical falloff zones.

You can also move, rotate, or scale your base geometry to line up to your bone system. Any changes made to the position, scale, or orientation of your geometry becomes permanent when you leave the Setup room.