As I understand the schematics (2015-11-29), the Sensors board has the following communications paths:
USB connector <-> FTDI <-> 96Board.UART0, which allows host PC to operate a console terminal on the 96Board (allowing running the 96Board headless and sans wireless).
ISP connector P6 that allows desktop/laptop with ISP programmer to program firmware on the ATMEGA from scratch. (Ie: this might be used to program a bootloader, but it is not the usual way to load sketches from Arduino IDE.)
96Board.UART1 <-> level shifters <-> ATMEGA.RX and TX. So this implements the usual way to communicate with the ATMEGA/Arduino for Arduino IDE purposes.
This implies that to program the ATMEGA, the Arduino environment has to run on the 96Board, which in turn implies that the 96Board is running an OS that can do that, and that it has the necessary hardware (such as a screen) attached to it. That's certainly a possibility sometimes.
However, I suggest breaking out the UART0 connection between U4 and ATMEGA, and also the UART.RTS (reset) line, to a header which can be either jumpered to the current configuration, or alternatively connected via an FTDI cable to a laptop/desktop to permit conveniently programming the ATMEGA from Arduino IDE on this separate machine. This would make it unnecessary to provision the 96Board for Arduino IDE.
Does this make sense?