got 94 of the 100 flags outside the cities, I know where to find number 95, but after that I must travel to the dark places in hope of finding the last 5..... killed 40 templars of the 60, but havent realy search the cities for them (have searched outside, I think theres 30 outside and 10 in each cities (not counting the starter town)), theres 3 cities with 100 flags in them (acre has 3 different flags), + 100 flags between the cities, and 20 in the starter town...
Hunting the flags & templar is easy, but time consuming ^^
and yes, all the secrets achievemnts are story based.. and since this is a assasin game try to guess how you'll get them :P
Edit: The flags and templar hunting "forces" you to explore the areas you normaly wouldnt go to during the story