You will likely burn out your Smart Junction Box (SJB) if you try to power your halogen headlights off the factory HID wiring harness. The HID ballasts are driven off of FETs within the SJB, whereas the halogen system uses relays powered by 20A fuses in the Battery Junction Box for each headlight. The relays are driven by FETs in the SJB, so you may be able to get by with adding relays and manipulating some wiring. Are the new headlights you got projector beam? Because if so, they use shutters to switch between high and low beam rather than having a separate filament for each within the bulb.
On the HID headlights, there is a power wire for the ballast (pin 9, hot at all times via a 20A fuse), a low beam control for the ballast (pin 8 that is controlled by a FET), a ground for the ballast and shutter (pin 11), and power for the shutter (pin 10 from high beam relay in SJB). The wire colors are different for right and left, but the pin numbers are the same.
For the projector beam, there's power for the bulb (pin 3, fed via headlamp relay controlled by low beam FET and a powered via a 20A fuse), ground for the bulb (pin 2), ground for the high beam shutter (5), and power for the shutter (pin 4, hot on High Beam).
-Rod