If i have the flag of the bloodkeep and a vampire with MR2 do i get a 2+ ward save vr shooting from wood elves with their magic shots/
Depends on which shots you are talking about. Most WE I know of swear by Hagbane which is the poisoned arrows, so you'd just get the 4+ against that.
2+ against Magic Missiles and direct damage though is insanely awesome protection for your Blood Knights and will keep them alive so much longer, then once they're into combat they should mow through most things, especially if you've got a Blender with them. Nice.