I have the Spyder2Express and a dual screen mac. It's a bit of a pain in the you know what, but it is possible to calibrate both screens with it. The 3 and the new software adds a bunch of whizbang features that do all sorts of automatic magic to your display. That would probably break this process. But if you don't want all that, and disable all that stuff, then it will probably work.

1. run a calibration on whichever screen is your main display (it's the one with the menu bar and dock).
2. go into the profiles directory ( /Library/ColorSync/Profiles/Displays/ ) and COPY the profile it just created. I rename mine with "LEFT" added to the end.
3. go into the system preferences, display settings, and change which display is primary (arrangement tab, drag the white bar at the top to the other one)
4. run another calibration. This time it will be on the other display.
5. go rename that profile too.
6. put your primary display back.
7. in the color tab of the displays preference on each monitor, pick the profile you renamed with the Left and Right names. You can use the Open Profile button to bring it up in the ICC wizard to see which is which.

Again, that's what I do with the spyder2express and the previous level of software... YMMV with the 3 and the current stuff out of the box.