As far as I know, only MAME games are supported at this time. I believe Thom was working on other systems, no idea on current status.
Not sure if you are using 710 or 810 alpha, but in 710 I have to plug a usb joystick controller in before I start a game, then it seems to work fine. I have both a wireless and a wired controller, no problems with either one.
tip: once you get it going, go into key mapping in mame and map "insert coin" and "p1/p2/etc start" to controller buttons. Both of my controllers have a select and a start button so I used those.