If you had 3.1, it would tell you what version you had when you first powered it on.
If you had 2.5, it would tell you that version when you entered config mode by holding SHIFT at power on.
I was able to upgrade from 2.5 to 3.1 by putting sio2sd.bin in the root directory of the SD card, entering config mode with SHIFT, and then pressing SHIFT-K3. This took a while because I got K3 and K2 confused.
The upgrade was successful, except that I can no longer select disk images from the Atari 800XL. I installed a default boot image, which kinda works, but when I select a new disk image to boot from, my selection is ignored and it just boots whatever it was going to before.