Well I use the parametric EQ in Sonar. I take the lowest band, boost 18 dB, and sweep forward and listen to the sound get muddier and boomier. When it starts getting mid rangey I stop and dial it back a bit. That's more or less the mud. Cut that however you see fit. The more you do this the quicker you can find the optimal range to low cut.
Kick and bass is harder since the low end is hard to get right. 250 Hz is a problem spot for kicks (stuffiness). Sometimes you cut it a little, sometimes you need huge cuts. Bass can have a resonance in the 150-250 Hz range, if you locate it you can cut it a few dB to make the bass less obtrusive.
If you take care of any unpleasant freqs in the lower mids/bass you've won more than half the battle. It's really something that comes with practice.
As for where to start, I start with anything that is easy/obvious. This totally depends on the mix and sounds in question.
But I'm hardly an expert so take all this stuff with a grain of salt.