Usually if you use a software that support multiple monitor, it will automatically load for you eg. Spyder3Elite, Coloreyes Display Pro.

For Spyder3Express it will only calibrate 1 monitor and load the profile to one only.. so what you can do is after getting both profiles, save them then disable Spyder's software. Then manually set your profile to each monitor so Windows will automatically load those 2 whenever you boot your PC.