If you are taking the time to make a custom PCB, you might as well integrated all the necessary components onto the PCB.
If cost is a the reason you don't want to integrate the ATmega328 and associated parts, consider the following. PCBs are charged by area used. So you are paying for the PCB whether the components are there or not. You might as well put the components in.
Also, if you design for a smaller board like a Pro Mini, people buying your kit will probably have to buy the Pro Mini as well. So their total cost is going to be the same.
I have used ExpressPCB's fab process in the past. While it is fast, it is very expensive. Now I get all of my boards from SeeedStudio. Depending on where you are in the world, it can take up to 4 weeks to get the boards but you get 10 5cm x 5cm for about $20 ($10 plus $10 for shipping). I don't know if ExpressPCB can export Gerber files, if not, then you might be locked into their service.