The BOS file that describes the animation of a unit is compiled into a COB file using a utility such as Cobbler or Scriptor. Both the BOS and the COB files are found in the scripts directory of your UFO or HPI file. The COB file is the actual file that is used by Total Annihilation, so you may omit the presence of the BOS file from your final UFO or HPI file if you wish to keep the guts of your unit a secret.
The COB file is binary in nature and cannot/should not be edited manually.
When generating your COB file, make sure that all include files you will be needing are in the same directory as the BOS file you are compiling.
For people wanting an in-depth specification of the actual file format, you can view these two documents: