Answering my own question in case it helps anyone else..
I tracked down a manual in German and translated a few sections after a few educated guesses, not sure if there's a better way to do this but I can search the entire SD card now using these steps:
1. Press right arrow to switch to the 2nd mask (for some reason the next step doesn't work if I'm on the 1st mask)
2. Press ctrl+left/right arrow to jump to the beginning or end of the mask string
3. Type in your search mask, e.g. RAIDERS*
4. Press ? to begin searching all folders, a search message appears on the display and the sio2sd leds light up until the search is complete