After downloaded and installed the free MKV Converter, launch this freeware (mkvmerge GUI) and click button to load video file.

Highlight the MOV file and click button just as screenshot below.

Select the destination folder with pressed.

If you want to attach any other file into the output MKV file, there are also some options to do it. Cause the MOV format doesn't support subtitle adding, we chose a subtitle file for the trial.

Going into the tab to add the attachment by clicking button. And never forget choose a file type under "MIME type" for the attachment like this:

Of cause you can merge more other files as output, just press the button to repeat steps above.

You can also choose to split the output file with huge size inside into more little ones. Just press into the tab, and select a proper size option under "...after this size" after activated the "Splitting" section and "Enable splitting..." as below.

Right now, you can start converting MOV to MKV by click button. And the converting process will be visible like this:

Want more about MKV converter, you can find them at http://www.mkv-converter.com.