If your screen isn't lined up with the outside on the PCB silkscreen, you may want to adjust it so it's properly lined up with the cutout in the enclosure.
A Panavise Jr will help hold the PCB in place while you solder. Place the PiTFT PCB into the Panavise Jr. with the header facing out.
Position the PCB so it's in a comfortable orientation for your hands to solder (lefty or righty?). Heat up your soldering iron, and grab some solder. Apply solder to the pins.
Check that all the pins are soldered nicely and there's no bridging, cold solder, shorts, or unsoldered pins.