I am interested in using this board https://www.sparkfun.com/products/9056 to switch between 16 inputs. I am currious as to if the VCC and S0-S3 need to be the same voltage? I was hoping to use a microcontroller that uses 3.3V logic but i already have a 5V line run to where this will be, will it still function if the VCC is 5V but the inputs to S0-S3 are 3.3v?
As long as VCC is a higher voltage than your I/O, you should be OK.
Ideally they would be the same voltage, but 3.3 volt logic is close enough to 5 volt that the board should be able to figure that out.