I run multiple WoW accounts on the same Battle.net account without problems.
Did you enter the respective account name ("WoW2") in the "BattleNet Account" field?
The Archaeologist still does not fly.
15:39:16 - [Archaeology] Go to Digsite Ruins of Ordil'Aran (distance: 6137,862)
[D] 15:39:16 - [MovementManager] You try to use flying/swimming path but you cannot fly/swim here, try to use ground mouvement...