Ok let's say I want to harmonize a guitar part and I want to use minor 3rds...my understanding is that you count the thrird note in the scale from the note you are harmonizing....right?
so, if I am harmonizing an E,D,F#,C do I take the first note, E, then use the third note in the E AEolian minor scale to harmonize it, then the same for D, F# and so forth?

And what are some other dark sounding things to do when harmonizing?