First things first: make sure your bike has a Wireless Unit (EW-WU110/EW-WU111). It is an optional component and most Di2 bikes do not ship with this unit installed.
In order to enable you to connect to the bike, press the button on your junction box for about two seconds (until the red/green lights start flashing). If this doesn’t happen at all, try updating your firmware. The SM-EW90 junction box (that’s the below-the-stem version) should be on at least 3.0.4. Connect the bike to a windows pc to make sure it is up to date.
If this does not solve your problem, please contact us and we’ll try to help the best we can!