I have them both.
Depending on which version of the PTLE software you have, you can't really access the Digi 001's midi ports. [Check at Digidesign User Conference for that info] However, if you are using Pro Tools, or for that matter any other sequencer, everything will be in sync.[Search here at MPC-Tutor for Pro Tools & MPC sync with Midi Beat Clock.]
I'm assuming you also have a midi interface connected to your computer that will send and receive midi with the MPC.
Peace.