I have, when needed, properly extracted the shit out of the mkv, edited the .ass in a Notepad, and then remuxed the stuff back into the mkv, not forgetting the new, better font attachment, naturally. But then again, I archive almost all anime I download, so it's easier this way should I ever rewatch the show.

I have used Aegisub to correct timing and turn a simple .srt into an .ass.