Activity Level and Pedometers

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My job requires a lot of walking, lifting, and pushing/pulling wrenches. It's a fairly active job and includes a lot of stairs, so recently I've started using a pedometer app on my iphone to track how far I actually walk each day. In my profile my activity level is set at lightly active, but I'm wondering if logging my calories from my pedometer AND classifying as lightly active is counting my "workouts" as double what they actually are. I don't want to be eating more than I should just because MFP thinks I'm walking twice as much as I actually am.

So to summarize, does the lightly active setting estimate the same amount of calories burned from daily activities that the pedometer is actually tracking? And should I stop logging my pedometer to keep a more accurate log of calories burned?