To get a kickass heavy guitar sound for metal try the following (check the following tracks for an idea of how this set up sounds)
'Flesheaters'
http://www.mp3unsigned.com/showmp3.asp?mp3id=9594
'The Futurist'
http://www.mp3unsigned.com/showmp3.asp?mp3id=29956

Rhythm guitars should have the gain/distortion at no more than about 7 on the dial, at the max. You get far heavier tones with less distortion.
Let most of the low end come from the bass guitar which should sit dead in the centre of the mix. Rhythm tones should be crystal clear and focus more on mids and highs rather than low frequencies. Aim for the lead and rhythm guitars to have different frequencies so they don't compete in the mix. Eg, if you play a lot of mids in your rhythms then your leads should have more highs and vice versa - (this is a very basic and watered down version).

Hard pan your rhythm guitars 100% to each side (make sure you record them in mono without any effects other than a little compression and some noise reduction. Add your effects (reverb, additional compression and EQ tweaks via insert VST fx) after the parts are recorded - unless they are integral to capturing the performance (tap delay, wah, whammy pedal etc). For extra heaviness, rerecord another set of rhythm tracks with any harmonies (5ths, octaves etc) with a different guitar sound or even different guitar and pan them from between 75% and 100% to each side. Depending on how heavy you want the rhythms, you can do another take if you wish with any accents for a centre pan track. Add some distortion in the post effects along with a little flanger and chorus (add to taste) to the bass and tweak EQ to add depth and heaviness to the overall sound. This is how I got the tone on 'Flesheaters' which is particularly nice IMHO:-) If you are playing an instrumental track with lead from start to finish you won't need that number of rhythm tracks - one to each side at 100% hardpan and one dead centre for harmony is sufficient while the bass takes up the low end. The biggest mistake most guys make is they get a real heavy boomy guitar sound that sounds good by itself then they multi track it and add the bass... this is the point things become irreversibly muddy. Take the low end out of the guitars and roll back the gain and you will get much better tone.

Hope that helps!