I launch it with the start.command and then terminal opens up does a bunch of stuff and then the server starts up, but the java console won't show up like it did when my server was just vanilla, no craftbukkit or plugins. But now that I have craftbukkit and a few plugins the console doesn't open.
Oh, that's normal. The Spigot/Craftbukkit servers do not create the GUI console.
Regarding mcMMO, when you say it doesn't work what do you mean? You get errors in the console during startup, or the features do not work, or something else entirely? We can assist, but need details to do so.