As for me, i keep mine in a magazine bag with magazine size backerboard. i also keep them laying flat, not upright in a box. Like I said though, that works for me.
I do the same thing...
The only reason I lay mine flat is b/c I don't have enough similar sized books to stand them up anywhere... same with vinyl... you don't want to stack different sizes lest the smaller books create impressions or rolls on the larger books.
If I had enough magazine sized books, I'd stand them up, but for now, American Splendor and TMNT are all I've got, so in a stack they sit.