Two things - subtle eq and setting the attack and release times on a compressor just right...I like to give the kick the lows, 40 or so and let the bass take over just above that. The exact frequencies depend on the style, sounds and most importantly the key of the song. I like to bring out some fundimental on the bass with an eq nudge. Sometimes it can sound good with lots of lows (30-50) shelved out of the bass. Then I will usually cut a little 300-500 out of both to avoid muddiness and find a nice mid spot for the bass to occupy to give it some presence.
Lastly I will try to find a "point" for the kick. This can sit anywhere from 2.5 to 10k. The idea is to almost meld the two sounds. The kick has the way bottom the bass takes over for the fundimentals and then the kick "clicks" on top. It's like bringing out the best elements of the two sounds to form one cohesive one.
Then the fun starts. I like to set a mid-fast attack and longer release on the kick to let the beater come through and then tuck in a little of the ring of the drum. Once that is set, the bass attack can be set so as to let it take over just as the kick comp closes down.
It is hard for me to verbalize but when you get it set right you can feel the two voices joining at the hip and the groove gets deeper..