On Gen I and II Vipers you can only align both "beams" of each headlight assembly at one time - so you align the low beams. Take the back off of the headlight assembly (which you undoubtedly did to install the HID system) and look for the two adjustment wheels - its been a year or two since I've done mine, but I seem to recall they are phillips-head-looking screws. One does horizontal, the other does vertical.
Personally, I park the car on a level street with another car parked about a hundred feet in front of me, and align the low beams vertically to get the license plate of the car in front, but no higher, and horizontally so they spread slightly. You have to stand in front of one headlight to see how you are doing with the other one. It works for me; I get good distance on my low beams (better than most factory settings, it seems), yet I don't get people flashing their brights at me, even with the HIDs.
Now, if you want to align the high beams, you are SOL. The high beams are attached to the low beams by screws and shims. So, if you get the low beams set correctly and the high beams are not acceptable, you have to take the assembly apart and change the shims. I'm in this situation now - my left high beam has been looking for squirrels in the trees since I got the car (and the right isn't much better). I've removed the left assembly and changed the shims around and got it closer, but its still high and to the left and thus needs more work, so I get to take it apart again sometime.
BTW: once you get the low beams adjusted correctly, you need to set the leveler (the thermometer-looking thing) so it is showing 0-bubble or slightly below, which is just a screw (torx?) beside the adjustment screws.