Check the picture! On the left breadboard (white plastic thing with holes) there are three trimpots. They change the voltage from the power source (be it a battery or external). Each of them has different voltage. When connected to an analog input of the microcontroller (right breadboard, blue thingy) the voltage is measured. This tells the microcontroller which output is connected to which input. The microcontroller then tells the computer trough serial port that a connection has been established, let’s say the LFO is connected to the oscillator’s frequency modulation input. The software on the computer (Max/MSP) acts accordingly.
The black chip underneath the microcontroller is a 4051 8-channel multiplexer. It adds further 8 analog inputs to the microcontroller, using only one analog input (there’s a great tutorial here). The final version will have 2×16 channel multiplexers. Due to the large number of inputs (plug sockets on the interface) and potentiometers the use of multiplexers is essential.