In addition is skirmish marks, some defeated foes will drop Bounties. Sell these - they are the chief source of coin from skirmishes.
You'll also notice various kinds of skirmish marks in your bags. "Skirmish Marks" are rewarded for achieving specific goals within a skirmish and for completing some skirmish related deeds. These are the main currency of all things skirmish. The skirmish camp barter vendors will trade gear and other goodies for these.
In addition, you'll get special marks for your efforts.
Rank Marks, such as Footmen's Mark or Veteran Guardsman's Mark are not used in barter and can be exchanged for regular skirmish marks.
Campaign Marks drop in specific skirmishes, usually from optional encounters. The tooltip will tell you which ones.
Challenge Marks, such as First Mark or Veteran's Third Mark can be looted in skirmishes of the right level and group size and are used to barter for the most exclusive rewards. Again, see the tool tip for more information.
Any special marks you don't need can be redeemed at the Skirmish Exchange vendor for regular skirmish marks.