How can I safely prepare bones for crafts?
Any bones which are obviously clean and free form any residual soft tissue shouldn't be too much of a problem. With skulls you obviously have more cavities to work about but if the outer surface is clean when you find it it is reasonable to amuse that the interior is too. 

Once the bones are cleaned of any soil etc a wash with dilute hydrogen peroxide should effectively sterilise them without damaging the bone. 

Obviously with any organic material of unknown origin you can never say it is 100% safe but equally it is ether practical or desirable to attempt to live in an aseptic world. For carving bones sensible precautions wold include wearing a dust mask (if using abrasives or power tools) and maintaining sensible hygiene in you work area. Similarly sealing your finished carving with oil, wax or lacquer should be effective in making it safe to display.