The opening sentence of the supernatural ability trick shot implies that the effect only affects the zen archer monk's attacks and, for example, the special ability doesn't enable him to see clearly through fey mist, and creatures can still use such concealment to make Stealth skill checks so as to hide from the monk. The zen archer monk simply makes attacks normally (that is, without any miss chance due to concealment) if he knows at least one square his target occupies.
For 2 ki points his attacks ignore total concealment and cover
This is much weirder because the zen archer monk "can't attack an opponent that has total concealment, though [he] can attack into a square that [he] think[s the opponent] occupies." Line of effect, however, is still necessary. Like the previous ability, only the monk's attacks—not the monk himself—ignores this total concealment, so the monk won't be able to see distant targets within, for example, the effect of the spell obscuring mist, but if the monk can determine the foe's square, his attacks can be made against that foe normally (that is, without the miss chance). While any archer should've already invested in the skill Perception, such an investment becomes doubly worthwhile for a zen archer monk.
That the zen archer monk's attacks ignore cover is more complicated. Presumably—based on the effects of spending 3 ki points—, this means any cover less than total cover, like cover, partial cover, soft cover, and cover creatures provide to other creatures by being in the way. The zen archer monk makes attacks against creatures with these kinds of cover (even if the cover's improved) normally, ignoring the foe's bonus to AC because of the cover. As some kinds of cover can be used by foes to make Stealth skill checks to hide, too, a zen archer monk's awareness of his foes isn't assured, so the monk may still be left guessing squares. Also note that these kinds of less-than-total cover don't usually block line of effect.
For 3 ki points his attacks ignore total cover
It seems as if the zen archer monk's attacks no longer need line of effect to his targets, as he can "even fir[e] arrows around corners" (which normal folks can do, too, but this is likely intended to mean the arrows travel around corners after they're fired not while they're fired). Likewise, making an attack against a target to which the zen archer lacks line of effect usually means the zen archer monk also lacks line of sight so the target will have total concealment—which the zen archer monk also doesn't care about. Thus the zen archer monk need only know one square his foe occupies to make attacks against the target. Presumably, the zen archer monk must know the path the attack's to take, and the attack suffers range penalties normally. How the zen archer monk comes to know this information is an exercise in employing the right combination of special abilities, spells, and magic items. That is, despite its high cost, without an effect like comic-book-style X-ray vision (q.v. the ring of X-ray vision) and maybe a successful Knowledge (engineering) skill check, the zen archer monk might only rarely find an opportunity to use this ability.