Di2 has a couple of options that take care of this issue:
You can choose to automatically shift the back up or down when you switch the front up or down.
Or, my favorite mode is to let the front shift automatically when the back gets to close to either side AND then adjust the back at the same time.
With this last mode it is possible to go through all gears with just one shifter, you only have to say if you want it lighter or heavier. It can be fully programmed at which point the front shifts. The other shifter can then be programmed to command the garmin device.