I always bend down (except for the e and B strings) because I feel stronger and more comfortable that way. Is there a proper direction to bend, or is it really just preference?

Except for the e and B strings that will go off the fret board when bending down of course.
I bend which ever way they'll go without going off the fretboard... I have no preference.
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whatever sounds better, usually bending up to another pitch sounds better so thats what i do, but sometimes if I find myself slightly past the blues note, I just bend down to it.
Basic rule, as said before, always towards (and past) the middle of the fretboard. Of course you may want to mix it up a bit from time to time, but mostly it's like that. No reason to bend down a G, you'll never get as many steps that way as you'll get by bending it up.

Kill bad habits! It's easy, really, just 5 minutes of frustration and 20 minutes of practice for a week and you'll be bending the right way no problem.