hi forum, not very often I'm back around these parts but i've found myself at a loss again.

I'm looking to capture a few bits of a Sky+ HD box before the box is replaced with new. I've got a hauppauge hd pvr box so my plan is to capture in 720p.

My initial test this afternoon I used the xbox preset which gives mpeg4 output and it worked fine, but most of my video collection is mkv. I'm familiar with using handbrake which is how i've converted my DVD TV Shows to store on a media server but i've always used mkv.

Is there any benefit from using mkv over mp4 as a file type? Don't both encode in h264 formats?

Ideally I'd like to capture the whole show in 720p, drop in an editor to remove adverts etc and save to my media server but i'm not sure which file / output will be easiest to work with as i'm not really done any editing before (nothing other then basic virtualDob avi stuff years back)

any advice / pointing in right direction will be appreciated