Yeah that can happen, if the games are running fine there is no reason to mess with the graphic settings, if you do have too just open the game's dosbox.conf which is loctaed in the game's folder and alter it manually by opening it in notepad and changing the setting on the line Output= to another setting like Overlay, DDraw, opengl, and Surface

You'll find shortcuts to the game in the Start Menu, and on the desktop too if you chose that option. The graphic mode setup tool must be run from the Start Menu; running it from the game's folder will not work.