I know Blizzard introduced marking flares a couple months ago, but for the life of me I can't figure out how to use them. Any clues on how to use them?
The raid leader and/or raid assistants can use them via the raid leader interface, which is accessible by clicking the tab that hangs out on the left side of your screen when raid frames are active. They're called "world markers."
With the new "War Games" option for BGs, would we be able to earn BG achievements if we're playing against our own faction? Like say if our guild split into two teams in order to work on "We Had it All Along *Cough*" or "Alterac Valley All Star" and the like - could that be done in War Games mode?
Nope. War Games give no honor, no XP, no achievements, no nothing.
While using the RDF tool last night I was put into a couple of instances that I had never run before but they had already downed the first boss. As a result the quest for that dungeon weren't available to me and they were unable to share the remaining quest. Is there a way around this or are you just out of luck until you get a fresh run? Also in another dungeon the group fell apart after one wipe leaving me with the quest for the 2nd boss, can I just pick this up again the next time I'm there?
You're out of luck for completing most introductory dungeon quests if you get Dungeon Finder'd into a half-finished dungeon, yes. But you can always run it again.
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