Don't close the back of he amp - it'll get too hot! Try an extenion cab, a Boogie Thiele cab would add lots of bottom end in a small package, or check out the Genz Benz G-Flex
Settings - on the single channel JCMs which I use I have 2 settings, gain at 7, Bass full, mid7 treble6, presence 2-3, that's for lower gain. Second Gain full, Bass Full, mid about 6, treble 7 , Presence 2-3 and boost with a pedal.
Now, there's a treble cap on the gain control in JCM800s, I think your amp will be the same. What it does is keep some reble in the tone at all gain levels, but I find it a bit too much, if you remove this cap it looses a bi of top and warms it up a bit when you're using less gain - but you'll stll get the same tone at full volume.