Hardcorde Subtitles to 3D mkv file

Ok so I have a problem that I have no idea how to fix. Usually I have Blu-Ray rips in mkv and when there are subtitles needed I just use mkvtoolnix to hardcore them to the file so that I don't have to bother turning them on when I want to watch the movie on my Blu-Ray player. Problem is I have an mkv file movie that is in side by side 3D. I'd like to play this movie on my 3D TV through my 3D Blu-Ray player, but the movie requires subtitles. I have the .srt file for the movie but it is formatted for the 2D version of the movie so when I turn on the subtitles they show in the middle of both side by side pictures, which will cause a problem once I set my 3D TV to the 3D setting and it merges the two images. I posted this in the mac section because I'm using a mac computer and figured this would be where I could find the most knowledgable help. What I'd like to do is make it so the subtitles show on both side by side pictures so that when they two pictures merge the subtitles match up and are readable. If anyone knows a way to fix this could you please help me?