For bass...
I know this is somewhat subjective, but getting the kick drum and the bass to work well together is so important. I like to think of it as one needs to be "on top" of the other. If it's a fatter, rounder sounded kick drum, I will try to complement it with maybe a punchier bass tone. If it's more of a sharp attack kick sound, I may go with a rounder, fatter bass sound. I think some people make the mistake when they want a real fat sounding low end, they go for the fat kick drum and the fat bass guitar, which ends up just creating mud.
I generally have less control over the kick drum sound since I often use loops. On the bass, I like to put more focus on getting the right tone up front so less has to be done with EQ later. This includes the right bass, the right pickup and EQ settings on the bass, and pre-amp settings.
After I've got a good tone and a recording I'm happy with, I almost always add some EQ with a HPF around 34Hz or so to remove any rumble or low end noise. I may end up doing a slight boost around 400 or 800 for definition but ideally I won't have to do this if I got a good tone up front. I will then add a compressor plug-in and usually set my threshhold settings to where the compressor is normally not triggering except maybe 20% of the time or less when I may have hit a note too hard.
Obviously there are a lot of variables based on the equipment, the style of music, etc. - but this is the basic process I go through when tracking and mixing. I know you can get a lot fancier with guitar mixing, but to me with bass for the most part I like to get just a good tone out of the bass and process it as little as possible.
On my Soundclick link below, the bass on "Deep Down Blues" and "No Mas Muerte" were some of my better bass tones where followed this process if you want to check them out. "Deep Down Blues" had a deeper bass sound "underneath" a brighter kick drum and "No Mas Muerte" is the opposite, with a deeper kick drum so a punchier bass sound "on top" of it.
Dave
www.soundclick.com/steakbone