There are so many options. Two things I can't figure out are graphic mode and scaling engine. Should I just use default settings? Which scaling engine should I choose? Thanks!

This is just a gui frontend for the dosbox options you can set in the .conf file which actually has comments describing what the options do. If you want a fullscreen that doesn't keep aspect, you can edit your config to use "desktop" as the fullscreen resolution and aspect false. Overlay for output and 2x scaler, the defaults, are fine.