Make backup copies of any changed files before and after your edits and keep the files in a safe place outside the MailServer installation folder.
To adjust the default font size for HTML messages edit the following file, ..\html\mail\inc\htmlarea\editor.js, on line 33 this.bodystyle = (to your desired settings), the default is Verdana x-small, which is 10pt.
The available fonts and sizes are listed in this file starting on line 54. To adjust the default font size for Text messages, you need to edit the following file ..\html\mail\skins\[skin name]\skin.css file, textarea font-size: setting. You will need to change this for each of the skins.