For the most compact installation, you can solder wires directly to the qik pins themselves and skip using the included hardware.
The included hardware allows you to make less permanent connections. You can break the 12×1 header strip into a 6×1 piece and two 2×1 pieces and solder these strips into the qik’s logic pins where you plan on making connections, or you can use a pair of pliers to pull out the two header pins in the original 12×1 strip for which the qik has no holes and solder the entire strip to the qik’s logic pins. You can see this latter approach in the picture below. You can then make your own cables that have female headers on them and plug these onto the male headers on your qik, or you can solder the pins to the other side of the board and simply plug your qik into a breadboard. You might also consider using a 0.100" right-angle male header strip (not included) for a lower profile.
The 3×2 header strip can be soldered to the jumper pins as shown above, which lets you make use of the included shorting blocks, and the included terminal blocks lock together to make a single, 6-pin strip that you can solder to the power side of the board.