Choosing Stepper Motor - Driver Combination
Sparkfun.com has some good tutorials on PCB design with eagle which is free. (with some restrictions). Upverter.com is also a good place to cut your teeth on, the learning curve will be slightly higher but less part creation which will save you time. As far as PCB design goes, make sure you have adequate power caps next to power hungry IC's. Find a PCB trace width table on the internet and make sure your traces can handle the current going through them. Typically you make big power\ground planes because it lowers the inductance and resistance of the copper on the board. You can think of each trace as a tiny resistor and inductor, you can actually calculate the values of each trace/plane. A big ground plane also gives a place for RF from processors or PWM to go to and makes traces less of an antenna. If your doing a two layer design it makes fitting the power planes into the PCB more complicated because you it forces you to run traces through your ground plane. This is where PCB design turns into more of an art, you are trying to balance multiple requirements. The picture here kind of illustrates this.

Start out by:


A ground plane on the bottom layer
Place your connectors and IC's, place them where it makes sense and rotate them to avoid crossover of traces
Route your power, using appropriate trace sizes
Route your digital signals (under 20Mhz, you probably need to worry about where they go too much, over that and it turns into more of a science)
You may have to repeat steps 2 through 4 and get better results


Then check the @#$^ out of your board before you send it off, make sure your schematic is sound, check all inputs\outputs and vcc and ground. Do they make sense? did you reverse anything? Did you get all the pins right and correct to the datasheets? 

Then check the PCB.
Are the pads the correct sizes on the parts? Do you need mounting holes? Do you want test points to make it easier to troubleshoot? (Oh and vias carry current, did you size those right as well?)

Then send it off, if it works 100% after you stuff it you'll be my hero.