Dark_Jedi, you can use megui to encode a great mkv. You can download it here:

That is the offline package so no need to install, just run it.

Once you run it make sure you are connected to the internet because it will look for updates. You will need these as it has a lot of presets updated all the time. It has a bitrate calculator, avs scriptcreator and everything you'll need and is very user friendly. I would use the script creator even if you are familiar with avs scripts. You can adjust the aspect ratio, scaling and everything in there.

There are many presets included. It all depends on what you want. I'm not sure if you can output an anamorphic mkv because there are a lot of players that don't recognise the anamorphic flag so would diplay it at the incorrect ratio. Your best bet would be to resize the video horizontally so you can keep the original vertical resolution. In the filters tab of the script creator change the resize filter to Lanczos4 as this is the best one. I've only ever encoded non anamorphic video to mkv with this program so its best to try out different options. I would also crop the matte bars off the video as this will reduce the file size also.

once you have created your script then you need to choose your encoder settings. In the drop down box you will see lots of presets. I usually use the bluray preset then change the bitrate to the desired setting in the config box. automated 3 pass encoding will give you the best results but will take a lot of time depending on your hardware. Once you have your encoder settings sorted you need to change the "file format" settings to MKV (or MP4 whichever you prefer) then just click on "Enqueue" and this will queue your render. Now you are ready to encode. Click on the "queue" tab and you will see all 3 passes queued up. Now just click start and your done.

Once your video is encoded you need to add your audio track. For this you will need Mkvtoolnix. Only use v3.2.0 because later versions are causing problems with media players, but this version works the best. It's best to get the gui for this program MKVMERGE GUI. It may be included with the download but i can't remember.

Just load your video into it first then your audio and just output your muxed video, it's that simple. You can change the video properties if you want but most players will ignore most of them anyway in an mkv package.