Most folks are surprised to learn that our prototypes are soldered by hand, often in our founders basement workshop. The fact is that powerful microcontrollers and low priced professional quality tools have made it possible for anyone with the inclination to design and assembly electronics using parts as small as the 0402 capacitor in our Input Box.
Believe it or not with a little practice you can solder this part too. The first step is to move from "Through Hole" parts to "Surface Mount" or "SMD" parts. These parts, as the name implies, do not have wire leads that pass through the board, but mount on the surface of the board. The advantage is lower inductance and electrical noise and a significantly smaller footprint. Eventually, as your projects get more complicated SMD parts become a requirement. If you've never soldered before Sparkfun has great getting started tutorials, but their SMD soldering tutorials are really stellar.
Naturally, these components demand PCB design software. We use EAGLE CAD, which offers a free version for makers and students. And of course, Sparkfun has our back again with some incredible EAGLE CAD tutorials. Once you have your design complete we love our friends at OSHPark.com, which is why all our prototypes are purple!
A good soldering iron is an indescribable experience. Wirecutter has a great write-up on the best options out there. We prefer HAKO, but some good friends swear by Weller. To really make professional boards you need a reflow oven. This hardware used to cost tens of thousands of dollars, but today an off the shelf toaster oven can be converted for under $100. We use Controloe and have nothing but good things to say about it.
Once you have an oven SMD soldering is surprisingly easy. Adafruit has a lengthy series of tutorials covering everything from solder paste storage to stencil making. It's well worth a look.