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I use ProjectX (java app.) to rip subtitles for a 256 or 4 color SUB stream rip. This makes a DVD idx/sub file. To make them work for the converted (mkv I assume) file I use BDSup2Sub512 (also java app.) . Just open the idx in the BDSup2Sub512 app. and only set free adjust (window opens after the file is opened) to .5 for x and y. Then hit OK. Then select from the menu EDIT, Move All Captions (if the subtitles are not already in the correct screen position) to what you find the best place on the screen. After this click the button "Move All" You can see the results in the split screen per subtitle. When satisfied use FILE menu to export. Add this idx (keep the SUB file until after muxing the subtitles into the mkv) in MKVmerge GUI together with audio and video and mux away.