MKR1000 Johnny-Five on c9 IDE

So I take it that the basic example in getting started is your issue and not the plant monitoring.

The actual ARDUINO sketches need to be uploaded with a suitable IDE than knows what target it is compiling for !

To try keep things simple use either arduino CREATE the online editor or the regular desktop version.
When you select the board it will then know what it is compiling for.

Some of the code mentioned does need a different compiler but NOT the Arduino sketches !
That may be confusing you.

Can you compile and upload the simple BLINK example from the Arduino IDE