Here's my setup:
I'm using a Sennheiser E-609 miced up to a Mesa Boogie 1x12 Recto cab loaded with an Eminence Private Jack. Mic position is just off-center. My mics go through a Blue Tube mic preamp and into a Tascam DP-02. I keep everything balanced and set my input level so that it doesn't clip. I take the .wav files from my Tascam and use Cubase to export the mixdown into an .mp3.
Here is kind of a quick and sloppy thing I just recorded real quick a few minutes ago to give you an example. There are two amps used in this track, the first one you hear is a Soldano Hot Rod 25 which is kind of a punchy 5881 based amp that has a nice, normal kind of low end. Then the 2nd iteration of the harmonized lead and the solo is my D-Moll which starts around 0:59. As you can hear, it has a huge low end. I have the bass set to around 11:00 and the depth set to about 9:00. I used a Diamond Memory Jr. in the FX loop for the solo and no other pre or post effects.
I also use Sony Sound Forge sometimes for quick editing. Both Cubase and Soundforge show the clipping meter right on the verge of clipping during the D-Moll lead. Here's the thing; if I go back and record it again but with the depth all the way off, the clipping level stays consistent, so it's like everything is cool as long as I keep the low end set very low.
It's not my mic positioning, not a bassy speaker, and nothing else. The tracks are all recorded at low volume but loud enough to where you can't really talk over it. My D-Moll has a huge amount of low end, more than any of my other amps. Other amps usually need a bit more low end at low volumes, but the D-Moll has a great low volume tone in my opinion. Anyway, here's the sample so let me know what you think I need to do to improve it.
http://soundclick.com/share.cfm?id=12821317