For a user, default settings for X apps go in ~/.Xdefaults. For example, here's mine, which sets some aterm settings:
aterm*saveLines: 50000 aterm*foreground: white aterm*background: black #aterm*foreground: black #aterm*background: white aterm*transparent: true aterm*transpscrollbar: true aterm*shading: 50 aterm*scrollBar_right: true