Hi!
Here is your biggest problem: The only app to be able to use the video card to offload decoding of H.264 video (one of the, if not the most common distribution codec currently used in HD video containers such as mkv and mp4) is quicktime X. QuicktimeX doesn't support mkv - so that means you have no ability to offload the decoding of that video file from the CPU to the GPU.
there are a several ways to solve it:
1) transcode your video to H.264 mp4 that Quicktime X will happily offload to the GPU
2) Transcode your video so it's at a lower bitrate. I have the most success with my 1080p footage if I limit the bitrate to 25000 and a constant quality of between 58-62.75% using Handbrake (to limit the bitrate, in advanced settings you add: :vbv-maxrate=25000:vbv-bufsize=25000 to the end of the string that's in the text edit box.
3) Try using Plex. Quicktime 7 (even with Perian) kinda sucks at playing mkv. VLC is better at playing mkv files, but Plex seems to work the best (you may still need to transcode to a lower bitrate).
4) Setup bootcamp and play the files in windows as most programs on windows will happily offload to the GPU for playback if the proper codecs (ie: klite) is installed (obviously, this isn't the best solution which is why I put it last
)