It won't unless the EQ is the first in the PC chain. It's something I and others have been commenting on for some time. In the thread bent4life has linked you to you'll see that Noel has commented that they are aware of the issue and are hoping to open source the mackie protocol.
Meanwhile an ACT controller if you have one will do the job. As you probably already know though you can't use the BCF in Mackie and ACT mode at the same time.