I don't have Green Day, or even USB instruments, but I guess it's the same deal as with earlier rock band games.
*from memory*
You'll need a cIOS that will allow both USB ports to work. Waninkoko's rev19 with a base IOS of 37 has it*, Hermes's cIOS v4 with a merge of 38 and 37**, and Hermes's v5 with the base IOS of 37 as well***.
*I'm using this one to play other music games from USB drive with the USB microphone plugged into the other port. Can't say whether USB instruments work the same way
**from this one, I'm not sure whether it works. I've heard it being advised often, but haven't tested it myself.
***this one works with uloader, but not with USB loader CFG. I honestly don't know whether usb loader GX properly supports v5 of Hermes's cIOS.