First I soldered the USB 3.0 micro female connectors for the controllers on the wires I had soldered on the main board. ( I used a breakout board to make the soldering easier. ) After some tests I recognized that the 4th pin / ID-Pin of USB 3.0 micro isn't usable at all. Now I needed a new 4th pin and found out that the shell goes through the wire as well. So I just used a piece of wire and connected the 4th pin with the shell.
Next I glued some short sticks on the bottom to glue the main board on it.
Next I glued the main board and the connectors on the bottom.
Then I needed a as small as possible power suply. I ended up with SATA. The problem was: where to get a female SATA connector ? The answer is: out of a broken hard disk.
Next I pulled out the pins i didn't needed, wired the connector with the main board and glued the connector on the bottom.
Then I glued the bottom on the rest of the cube and connected the LEDs with vcc and gnd of the SATA connector and data in of the first LED with pin 11 of the Boarduino.