In MTW skirmish, I believe the unit will only skirmish away from their target unit, so they may blunder into another enemy unit while trying to keep their distance. You will just have to micro them. I don't skirmish archers, I just move them in front of my troops, get a few volleys in, then pull them back when the enemy starts marching quickly.

The Highlanders weakness is a combination of defense and morale. Their low defense (-3) means lots of casualties, and on normal difficulty this will usually make them easy to break after the initial surge since their morale is 0. On expert, you can't rely on this, they will just keep dishing out damage. The ideal solution would be to use missile weapons, but their quickness means you won't get in many volleys before they close. You might have to resort to pinning them with your spears then shooting into melee.