2 track recording timing for remaining tracks

hello i have a question ok so i have a mpc 1000 and a m-audio fast track pro and im going to be tracking out beats 2 tracks at a time into protools 9. my question is when i track out the first 2 tracks and i want to record the next two tracks, is the timing going to be the same. because when you track out beats they say you should leave some space before the music starts and that will give the mpc or the computer time to sync up correctly. but i guess what im asking is will the timing be the same for the rest of the tracks. or will it be better to track out all at once ?

Or you can just connect all of the 1000's MULTI OUTPUTS to the M-Audio and track out 8 tracks at a time.