You're just at the bottom of a learning curve, and you'll get there. It may feel like you're a moron, but you're not -- you're just learning, adapting, and adjusting. Eventually it'll become more and more like a second nature rather than something you really have to think about all the time.

It gets better, really it does. It's not quite like re-learning how to ride, but you'll definitely have to re-establish your comfort zones. Originally I thought I'd never be able to ride on the road with these stupid pedals, now... it's just something I do. You'll get there, and you'll kick butt on all your familiar routes