I'm pretty sure the Pioneer setup (assuming there's a DJM-900 or something in there as well) has a far far far better audio quality circuit than your MP2. Ideally you'd be running Club Kit or an SL box in that location. The nice thing about Serato is that if you plug into the new setup, all your crates will just work natively out of the box.
I don't see any reason why it shouldn't work with a MP2 + 2 CDJ's though. You might need to install drivers though. Search for "CDJ-2000" on this part of the site and it should point you in the right direction :
serato.com