How to hear harmonies in your head. (writing a part for two instruments)

I have been composing for a couple months now and right now I am writing a piece for two guitars and a flute. I am working on a section which the flute is playing one melody and the lead guitar is playing a second melody underneath it. Usually if I compose a single melody I can hear it in my head, and i usually double check it with the flute, but now that I am writing two melodies at a time I cant hear the harmonies in my head. How can I tell if the two melodies will sound good together? (im not good at piano either)

Experience tells you which self-standing intervals sound consonant and dissonant, and further experience tells you the effect of different harmonic progressions. By interval, I mean the gap between the two notes.. so an E and a B above, would be a perfect fifth... an E and a Bb above would be a diminished fifth... these two have very different effects.

Some people can hear polyphonic music in their heads very well.. for everyone else, there's music theory. If you haven't already, learn the various chords of a scale (I, ii, iii, IV etc.) and you'll quickly get the hang of what harmonic progressions sound good.

I would start with some aural training, learn all the intervals up to an octave (thirds, fifths, etc.), then try to identify them without the notes written down. There are a few websites that provide written and sounding exercices for that. Then, you can learn (for more complex part-writing) the triads, the seventh chords, and after that you can learn harmony and such. Here's a great resource to help you get started:

http://www.teoria.com/

thanks guys, I appreciate the help :D