Whatever settings you have now should still work. Unless you have problems, I think Direct 3D is the 'best' rendering method. Software / Direct Draw can be a little slower, but in some cases avoid problems / glitches (in the council hall and with cut scenes) that some people have run into using Direct 3D.
After you run the configuration program and make any changes, you can select the 'Skip Test' box, then click on 'Test', then on 'Apply and Close'.