For Independents I always did Bones hard bottoms / Bones medium tops. Would take like a week to break in but then was perfect for a year and a half. I didn't really have any real rhyme or reason to that combo aside from "I usually blow out the bottom Bones after a while, so if it's harder maybe I won't."
Right now I'm skating a set of Ventures and blew through the bushing really fast. Out of necessity I threw in the alternate Bones combo since I had them laying around, so it's medium bottom // hard top. I think I've read that this is actually the more common way to do it. I don't know how I feel about it yet, but (off topic) TBH Ventures are still on "trial mode" for me right now anyway... just trying to tinker and see if they're for me in the long haul. I'm already kinda over the fact I have to tinker at all though because the whole idea from moving away from Independent was to find a truck that just feels good stock, because I've realized that skating a truck stock is truly the only way to avoid the madness. You roll with punches instead of concocting quick fixes for everything haha.