Hi Andy,
The examples for CC2540/41 use the analog voltage signal from the joystick ("JOY_LEVEL") to read the joystick. I beleive it is connected to P0.6 on the CC2540.
If you download the software examples for CC2541/43/44/45 and take a look at the document called Software Examples Overview (or something like that) you will find a table which connects signals from the EB to pins on the EM.
Cheers,
Fredrik