Here is a tone tip that I only recently discovered that has completely changed the way I approach all recording. If you can, use multiple guitars when recording. I'm lucky because I have a fair few axes so now I use one guitar for recording all rhythm parts, another for doing harmonies and a separate one for lead (neck and bridge). Sounds like a lot of hassle but in terms of geting different tones that actually each stand out clearly in a mix this has been a revelation for me. Anyone working off one guitar can improve things by putting an EQ pedal onfront of their preamp to affect the raw pickup tone for each guitar part - this works a lot better than recording everything off the same setting then tweaking with post EQ (been experimenting with that too recently). Of course, if you are using a PODxt or something like it you could use a different patch for each part but remember the characteristics of the pickups will be very similar regardless of the levels of distortion. Just thought I'd share the ideas.