Well not all blueprints are going to line up perfectly.
I normally take my blueprints into Photoshop and make sure they line up, and make all the necessary tweaks if they don't.

But allot of the time they don't line up, and your just going to have to compromise. I only rely on the blue prints to get the right proportions, and then use actual photo refs for all the details, and intricate shapes.

What car are you going to be modeling?