I have only used the two together in the same recipe, so I can't comment from experience on how different they are in taste. Some swear they are different, hence my use of both at once.
I did check Beersmith and Promash, and flaked rye is listed as having slightly higher extract potential than malted rye. So you should probably use the full 2 lbs of rye malt (or even a pinch more), I would think.
Best of luck on the brew! I have 15 lbs of flaked rye and rye malt I am just DYING to brew up (gotta stop travelling with work....).