As I understand it, could be wrong, the Bills use a cash to the cap system. Which I don't believe the linked website is using to determine the Bills cap numbers. I believe in that system any money paid out to the player will be applied to their cap.
Merrimans contract according to rotoworld:
http://www.rotoworld.com/player/nfl/3171/player?r=1
So $3M of his 2nd year base salary is guaranteed, so they're going to be paying him $3M this year regardless. Which in their system would be applied to their cap, so whether he is on the team or not that $3M is going to be hitting their cap.
As I said, this is how I think they work things, I could be wrong.