OK, a synopsis, basically what you do is you breadboard out the preceding circuit after ordering the parts from Mouser or Digikey or wherever (remember to also order your battery holders, any case and discretes like resistors and diodes...a lot of time I forget).
Breadboarding critical in that you basically proofread your circuit. Once its working the process of making the working PCB is a simple matter of physical transfer. In that, from a certain point of view, all you are doing is swapping your wires for traces. So when you have it working you do up the PCB traces on your PC and make your board.
Insert the components all in one operation. A lot of people dilly dally with it, but you have already designed the working circuit. If you mess with it, you'll just muck it up. Solder all in place and cut the leads.
Should look something like this when you are done.
Almost forgot...get the terminal block for your PCB like in the image. Makes your project look so much nicer, I think.