Sorry for the vagueness of my answers, but I'm at work and this is from my faulty memory.....
In the Windows control panel under game controllers (maybe devices>game controllers if Win7),
there is a setting to set the pedals combined or separate. It's a lot easier to find in XP.
In Win7, it's a bit harder to find.
I think you have to right click the controller or something to get to the calibration/settings window.
Or...... In logitech profiler, create a new profile. When you do that it will have you navigate to the exe that you want it linked to.
From then on, that profile will launch automatically when the exe is launched.
After creating the new profile, the option to combine or separate pedals is buried in one of the tabs at the top.
I'll edit my post to be more specific when I get home, but I hope this helps you now.