There are many tools for separating different parts of a segment. Get familiar with masking section, as it allows you to restrict what parts of segments may be edited and how.
For example, you can use Scissors effect combined with masking as shown here: https://lassoan.github.io/SlicerSegmentationRecipes/Craniotomy/
You can also use Paint, Draw, and Erase effects with masking.
You may also use Grow from seeds without any masking. Just add a segment for all “other” materials (soft tissue, air, etc.). If there is not enough separation between parts of the bone then you may need to paint more seeds interactively, while in preview mode.