shouldnt make that much difference if u keep the same internal volumes. i think it comes down to how flash the back of your subs look and the available space u have to put them in (if u mount em magnets-out, they r gonna reduce the depth available in the box, making the box long & skinny). and if they r in da boot of a hatch or sumthin, that will make things awkward when u wanna use boot space if they jut out. harder to protect from damage too
what sorta subs r they? wat car they goin in?
as for one in-one out, you will have to mount them out-of-phase or they will cancel each other out...out-of phase i cant imagine much of a difference from above acoustically speaking.
are you lookin for maximum-bass from them or just loud 'good-quality' bass?