Add moderate compression to distorted guitars and light compression to acoustic and clean guitars. Equalize the tracks to fit into the frequency spectrum, with rhythm guitars having more low midrange and lead with plenty of high-end definition. Add slight reverb or delay effects, but keep it limited--you don't want the recording to become indistinct.
Set a preliminary pan for each of your tracks. Set the rhythm guitars at about 30 left and right, with the lead tracks around 35 right. If you have more than two rhythm guitars playing at once, set them a few degrees away from each other--for example, two guitars at 30 and 32 left, and two others at 30 and 32 right. Lead guitars, particularly harmonies, can be panned opposite each other in the stereo field.
Adjust volume levels so that the rhythm guitars create a background harmony for the lead guitars. Make sure you can hear each instrument, but don't make it too loud, especially if you have other instruments to add later. Watch the peak meters and keep the levels from hitting red.
Add panning and volume envelopes, like fades or sweeps. These can be effective and even necessary to blend parts of songs together or to make lead lines more interesting. Consider varying the volume and pan very slightly on the tracks throughout the song to give a looser, more natural feel.
Add other instruments to your song as needed.