I have seen many mkv files with libebml v1.2.3 + libmatroska v1.3.0 as writing library. But when i convert my videos to mkv using ffmpeg with x264 codec the writing library is Lavf55.21.100 . How can i use another libraries while encoding ? Is there any difference between the qualities of both libraries ?
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The "standard" multiplexer for the Matroska container is mkvmerge / MKVMergeGUI (project: mkvtoolnix / bunkus.org).
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I can't imagine why the writing library would make any difference to encoding quality. If you use the commandline version of x264 and output directly to MKV the writing application will be x264 and the writing library will be "Haali Matroska Writer". Take that MKV and remux it with MKVMergeGUI, and MediaInfo will show the writing application as mkvmerge v6.9.1 and the writing library as being libebml v1.3.0 + libmatroska v1.4.1 (latest version of MKVMergeGUI).
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The writing library is responsible for creating the container, not the video content. One writing library may create a less complete container, or a container with a slightly different structure than another. Some players may be more or less tolerant to such differences due to a limited implementation of the Matroska specifications. Remember when mkvtoolnix defaulted to using header removal compression: marginal savings, major incompatibilities...