If you are running AB+, or don't have the config menu mod for some other reason you can still have some control over the mod, here are a list of commands you can enter into the debug console.
(open the debug console by pressing ~, then type in a command below and press enter)

SoundtrackList / ListSoundtracks / ShowSoundtracks
Displays a list of the currently installed soundtracks along with their ID numbers.

SetSoundtrack X / SetMusic X
Change the current soundtrack to a specific one, X can be either a name or an ID number.
e.g. "SetSoundtrack Flash" or "setmusic 9"

EnableShuffle / ShuffleOn
Set the mod to shuffle mode

DisableShuffle / ShuffleOff
Turns off shuffle mode

ShuffleFrequency X / ShuffleWhen X
Set how often to shuffle the music when in shuffle mode, X can be "room" or "r" to shuffle when changing rooms, "floor" or "f" to shuffle when changing floors, and "game" or "g" to shuffle when starting a run.
e.g. "ShuffleFrequency Game" or "shufflewhen f"

NextSoundtrack / Shuffle
Change the current soundtrack, if shuffle mode is off it will be the next one in the list, if shuffle mode is on it'll be random.