One thing I found which I must have missed in the documentation is that the Tuner mode will activate if you press the Up and Down bank pedals at the same time, good for a quick tweak without having to bend over and press the little, tiny button on the panel.
I used the Output button to best match the ME-33's output to my input source. Since my ME-33 was plugged into the effects return of my guitar amplifier, I selected "G.AMP". When recording direct or using headphones, however, I would have selected "LINE". This setting inserts a COSM speaker simulator after the GTR AMP effect block, emulating the important tonal effect that a guitar speaker has on the overall tone.