I'd wait until the device comes out, personally, then you may have a new built-in preset from the handbrake team to better fit the new devices. But, that being said, the current presets work just fine and the ATV3 will definitely be able to handle them just fine. Since you already have your films in an .mkv file, you can put them all in a folder and let handbrake scan the whole folder. It makes things go much more quickly than they used to be. And, before someone else mentions it, you may want to give this thread a quick look:
https://forums.macrumors.com/threads/805573/.
For SD content, I modified the current

TV 2 preset present in the file by simply bumping up the constant quality marker to 18 from 20. I also turned on the decomb filter for all encodes, as it helps reduce interlacing artifacts. For older DVDs, I usually enable the detelecine filter to further clean up the video. Using this preset gives me files that, on average, are less than 2gb in size, with most ranging from 900mb to 1.2gb.
For HD, I have two separate presets. One for films that are mostly well lit and colorful, and another for darker films (like Underworld, the recent Batman flicks, and the first two Resident Evil films for example), since those types of films exhibited more artifacts than the others. The first HD preset is a minimally modified preset of the SD one I mentioned; only added two extra reference frames in the advanced options. The second is more complicated to explain, so here's the advanced option string for it:
Code:
b-adapt=2:ref=6:bframes=5:me=umh:merange=20:no-dct-decimate=1
Some think it's a bit much, and I agree, hence why it's my 2nd option, non-preferred option.
Also, for your BD .mkvs, you may not need to re-encode the file at all with handbrake. If you're on a mac, download subler and drag the MKV file onto the icon, then save the tracks in an .m4v container, making sure the video profile is at 4.0 or lower. For your DVD .mkvs, you probably can't go this route, since the video codecs aren't supported in iTunes/

tv.
Lastly, for mobile files <1gb in size, handbrake had a target size field in previous versions, but it seems to be removed in the most recent version. You can always set a target bitrate instead, but you won't get consistent results. You could always track down handbrake 9.5.0 to re-enable the option, or just adjust the CQ from 20 in the

TV2 preset down to 23 or something.