Photoshop :: How To Erase Elements From A Layered File

I took a time lapse of 240 photos of the highway below. What I want to do is create a background plate where all the cars are erased from the shot. The steps I've been doing are:

Open photos A & B in Photoshop (I'm using CS6)Drag photo B's background layer into A as a new layer and line up with A using 50% opacity and eyeballing it (is there an easier way to do this? the photos need to match exactly)Start erasing in obvious areas from layer BMerge Layers when there's nothing else to erase Repeat 1-4 with a new photo.  

I don't think I'm doing this right though, because the baseline photo always has cars I can't erase. I can do the reverse, and take photo A into another B photo, but it just feels like the way I'm doing this is wrong.
 
Is there a cleaner, more precise way to do this? If I've added a layer with no cars on top of the background layer, shouldn't I be able to erase the cars from the background layer?