tracking mpc 1000 to the mbox 3 mini mic/line and line input

i have a question. ok so i'm going to be tracking out beats 2 tracks at a time using a mbox 3 mini and i was wondering. now the mbox 3 mini has 2 inputs, one is a mic/line pre amp input and the other is just a regular line input, so for tracking out beats isnt one input going to be better for tracking, should i track out the beats one track at a time using the mic/line pre amp input or just use both of the inputs. im not sure what to do here. wouldn't the mic pre/line input be just the same as the other if im only using it for line in and not mic recording. i mean i don't need the phantom power. please help.