Why not start out with a pencil and 0.1" grid graph paper and design a few small circuits just to see what you have to do in order to work your way around a crowded IC or if you have to use vias/double-sided boards or jumpers/single-sided boards. I started out doing manual PCB design and really, haven't progressed much from there as the program I use for design is not an autorouter but nothing more than a computerized version of manual layout.
I guess it's like a lot of things. Learn to use a hammer before using nothing but a pneumatic tool; learn the benefits of a simple manual screwdriver before depending solely upon an electric driver.