If handbrake is too complex for you, I'd try MKVTools 2.4.7
It's not free ($4.99), but it's pretty decent and a lot more beginner friendly. You can use it for free, there's just wait periods when opening video files, and annoying reminders to register it.
Sheepykins, MKV is just a container. No harm putting it in an m4v, just don't change anything else.