Add the alias to your shell profile.
Depending on your system, shell and local/remote connection, the file sourced(loaded) may change.
For BASH and Debian, you could edit ~/.bash_profile
nano ~/.bash_profile
It is common to get a mkv from youtube because the streams downloaded are not compatible with mp4.
It is easy to force the best mp4 streams though.
Add this to your shell profile file
alias youtube-dl-mp4="youtube-dl -f 'bestvideo[ext=mp4]+bestaudio[ext=m4a]/mp4'"
OR
alias youtube-dl-mp4='youtube-dl -f '\''bestvideo[ext=mp4]+bestaudio[ext=m4a]/mp4'\'''
Then you need to reload/reconnect the shell or source the profile again.
To use you can just call it
youtube-dl-mp4 <url>