Squier Jazz Bass vs. Fernandes Atlas Bass 4x
 

There's this store selling Squier Jazz Basses worth $210 each. All of them are good. Another store was selling Atlas Basses for $320 and I am looking for humbuckers. The only problem that I've got is this:

Should I stick to an old trusted brand (Squier) that sells jazz basses or to the one's with humbuckers (Fernandes)?

Try them both is about the best thing for you to do here. One of them will appeal to you, go with that one. Don't try to over-think it.

BTW, Fernandes has been around a long time too, and has a rep for being a "sleeper". There are more differences between those two than just the p'ups. Do some homework, and spend time with each as suggested above.