Archers - and to a certain extent other horse archers - are horse archer units' worst enemy. They are the best way to fend off horse archer armies (e.g. Turks, Horde).

When using Boyars I would recommend treating them as normal heavy cavalry with the added bonus of being able to shoot. When I played the Russians I hardly ever skirmished with Boyars, because they are simply too expensive to send in front of the enemy line to get shot up. Instead I used them on the flanks and shot at other units whenever they had the chance and then charged in when they were needed in melee. If the enemy has no archers available then skirmishing is a viable option. However, as you stated, Kommodus, they tire quickly when skirmishing which will reduce their fighting ability when they are needed for melee. In my opinion, Boyars are best when used in melee, so having them run around too much is not such a great idea. Just shoot a few rounds and then send the boys in to break the enemy infantry.

On another note, I once had a 7-star Boyar general with 13 valour. He had attack 15, defence 21 and morale 30. Needless to say he was unroutable, nay, unbeatable.