I'm using both block erupters and blue furies on the same instance of bfgminer.
Like previous posters have said, you just have to specify your devices. It's pretty easy to do on Linux. I'm using RedHat 6, but the process should be similar on Ubuntu. To find out where your miners are, run:
ls /dev/tty*
Block erupters show up as /dev/ttyUSB# and blue furies are /dev/ttyACM#
So your basic bfgminer command for 3 erupters and 2 blue furies would be:
bfgminer -c bfgminer.conf -S erupter:/dev/ttyUSB0 -S erupter:/dev/ttyUSB1 -S erupter:/dev/ttyUSB2 -S bigpic:/dev/ttyACM0 -S bigpic:/dev/ttyACM1
note that I've defined the blue furies as "bigpic". On Ubuntu I had to use "bitfury" but on Windows it was "BF1". I actually run 21 erupters and 2 furies. It makes for a very long command line, but I launch with a shell script so it's no more difficult than specifying 'all'.