I'm sure there are 100 ways to do this. But I do it like this
1. Make sure that the SRT-file is in UTF-8 format
2. Add MKV to Handbrake
3. Import SRT to handbrake
4. Choose the checkbox "Default" leave the others empty unless you want to burn the subs into the picture. Then also check Burned in.
5. Make sure that SRT language correspond to the default setting in ATV2. In my case Swedish (not necessary if you burn the subs)
6. Set char code to UTF-8
7. Click Add in subtitles tab
8. start transcoding