Step 7: Solder paste the rest of the pads
See the diagram; It highlights all the pads. There are some pad looking areas that don't need paste. They are marked. Don't panic if you paste them. No harm done.
Concentrate on just getting some solder on every pad. Surface tension will suck the solder into the center of the pads pretty well. You can fix it up with some wick and soldering iron if there are bridges. Go very sparse on the Atmega and FTDI footprints and more generous for the other components.
Use the sewing needle to touch up or clean up any spots where the paste didn't go quite right. Be gentle with it, but you can clean up the paste with it pretty well. You have a really wide tolerance for the amount of paste that will work.
Use a magnifier and inspect your work. Gently use the needle to clean up any messes or bridges. Don't worry too much about perfection. You can clean up problem areas with a soldering iron later.