Sounds like a good method, but only if your positive you like that effect. Most guitarists will also run distortion at the very end of the effects chain, after the modulation like phaser, wah, chorus, or flange. The audiotool distortion isn't that great though.
i always run through an fx pedal w/ cosm (modelling) so i can get the desired (necessary) distortion before going into the mixer. :) the only other way i might is mic the amplified speaker.
The mixer is powered, so no need to pre-amp it. I could mic a bass cab but I run my bass right into the board for now. I use the stereo tape out rca plugs through an adapter into the soundcard stereo 1/8 inch plug. I'm also making my samples with Adobe soundbooth now for better sound, although I need to lower the quality to upload lol.