I didn't use any of them, but I'd guess the active archery skills replace the normal damage. To check that you could save before attacking an opponents just with the bow, then reload (if it is not tough enough to take a few shots) and use the skill.

I didn't test the rate of fire using arrows and skills in order to compare, but I would think the recuperation time is used.


Archery as a warrior - my thoughts

Note: in the disk version of the game True Shot and the damage portion of Crossbow Expertise are broken; they are fixed in the download version.
The weapon expertise skills were also changed to all give a percentage damage bonus, which may make a difference with some of the comments in the topic above.