I install all my boxes first. Then I run my 220 lines, then my dedicated 20 amp lines for things like the microwave and other power hogs. There are two ways to power lights, either go hot to the switch, or hot to the light, and then run a line to the switch. I always make the switch hot so it's easy to install or change the light without having to turn the power off at the breaker box. I also like to give each room it's own breaker. It's cheaper and faster to run power to a common wall and have outlets on either side, but it's easier to do stuff in a room if one breaker kills the power to all the outlets in that room. Some people also like to put the lights on a different breaker then the outlets so you can still see if you blow a breaker. There is no advantage to running 12 gauge wire for your lights if they are on their own 15 amp breaker. It's cheaper and easier to install all your GFCI outlets right next to the breaker box, and then run your lines to their locations from there. Its common to see a dozen GFCI outlets right next the breaker box in new construction.
