Clipping is definitely not always a bad thing. In fact, I would say it can be a very good thing on almost anything that's not chords. What you don't want to do, however, is have your sounds running hot into the master, that's going to cause you problems. To avoid this, you can take any common household limiting plugin like Ozone Maximizer, set its attack, release, lookahead, whatever, everything to zero and then limit away, it's essentially the same as clipping your master, and on top of adding grit to your sounds, it's a very nice way to get the perceived volume of your basses up and keep your levels in check. Just don't overdo it.