For Accuracy's Sake

How are you liking psychology?

Alrighty, here's a run-down of the situation:

I'm a college student on a huge campus, so during the week I walk a lot from class to class. Now that I live off-campus, I'm walking even more just to get to campus and then get to class. However, on the weekends I don't walk nearly as much.
I don't want to set my activity level around how much I'm walking, since on any given weekday I could walk a few miles, but on the weekends I might only walk one or so miles at the most. So I've set my activity level on MFP to sedentary, and I've been keeping track of how much I walk (with a pedometer app) and logging it on MFP.
I also run, but I log this separately and turn off the pedometer app so I'm not double-counting exercise.

Anyway, my question is, do you think this is a good idea? Or is there a more accurate way to log this kind of stuff?

When you have varying levels of daily activity like you do, I find it's far better to use a TDEE method for achieving your goals. You estimate what your weekly TDEE is and eat calories at an appropriate level in relation to your goals. If weight loss is your goal, eat 500 calories below your estimated TDEE and track your results. After a few weeks you may need to raise or lower calories based on results because your TDEE is always going to be an estimate. When you try and track calories eaten, calories burned through walking, calories burned through exercise, etc you are introducing a whole bunch of variables with different degrees of accuracy. Using the TDEE method keeps it's simple. You have an estimate of what you burn each week, and an estimate of what you eat. If you aren't losing weight you simply increase what you burn, decrease what you eat, or both. Do just the opposite if weight gain is your goal.