As far as I know....you can't do what you're asking. If you have your pedometer on "all day" mode, then it's going to track all of your steps, and won't make any differentiation between your regular, everyday steps and the activity you do specifically for a workout.
Personally, I don't even bother to wear my pedometer unless I am specifically going out for my walk, the one I count for my workout. I have my pedometer set to "active" mode so that when I put it on before I go out, the number of steps I have to take before I earn a point is lower.
So yeah..I don't think you can "have it both ways" with the pedometer. Of course, I could be wrong, but...I'm pretty sure I've asked a question similar to this before and gotten the answer that "no, you can't do that".