I’d like to transmit digital sensor readings (two inputs) from one XBEE platform board powered by 9V battery [2] to another XBEE platform board connected to a PC [1]. The one sensor connects SO/CS/SCK > AD3/AD2/AD1 on the XBEE; the other connects IN_RX/IN_CTS/OUT/TX/OUT_RTS > Dout/CTS/Din/RTS.
Can I test remote sensing entirely with AT commands? Is there an example on the web?
If not, I assume that I’d have to set [1] to API mode; program [2] to wake-up regularly and transmit a frame from sensor 1 and 2, hopefully not at the same time. Is there a worked example of this on the web?

if I am understanding what you are saying one sensor will connect to the Analog inputs where as the other sensor will connect to the UART pins. If that is correct, you will need to use ADC mode on the module that is connected to the application that is receiving the data. The side sending the data can be in transparent or AT mode.