I have a similar set-up (mbox 1, midisport 2x2, G5 iMac, mpc, triton and other modules.) and I have been recording beats like for the last four years that I've been using Pro Tools LE.
First completely sequence your beat in the mpc.
Second save your sequence as a midi file.
Third, import you midi file to track in pro-tools. I'm not sure if you have to, but check the box that says import tempo map from midi file.
Fourth, assign the MIDI tracks' outputs and record track by track.
Basically you make your mpc into a sound module and Pro Tools into your sequencer. Be sure to name your tracks and switch the ones controlling modules to "MIDI" and leave the sample tracks as "drum." By doing this I've never had to trim tracks, start four bars in or anything else but record and mix. Combine this with the grid edit mode and it's the sh__! Not to mention, your midi file is right there which makes the remix a breeze.
Sorry for such a long post, I hope this helps...Cheez