The main thing is picking kicks and subs that do well together. For example, if you have a sine-wavish sub bassline, then picking a clean 808 kick, which is basically the same thing with a click at the front where the waveform starts out of phase, is going to cause problems. You can avoid 95% of kick/bass problems just with sound selection.
I would urge you not to resort to the common "trick" of low-passing the kick. That's a total nightmare and I don't know how that notion ever got started in the first place. If anything, you want to boost the high end if your kick can't cut through the bass. When I mix records I frequently gets hip-hop songs with kicks where the producer went ahead and low-passed it. Drives me nuts. I think they are all watching the same B.S. youtube video tutorial with horrible advice.