Start by shifting both the front and rear derailleurs into the smallest sprockets.
Un-thread the Easy-Split cable separators and pull all the cables out of the cable stops (pay attention to which cable goes where).
Pull out both seatposts.
Remove both wheels and pull the quick releases out.
Unbolt the rear derailleur from the frame and put it in an old sock. You can leave the drive chain attached, just be careful to protect the frame and avoid kinking the chain.
Remove the left crank arms. You can leave the right crank arms attached, but it will pack easier if you remove them as well. The timing chains will fall off when the left crank arms are removed.
Remove the front and rear handlebars at the stems.
You may have to remove racks and/or water bottle cages.
If you have a disk brake unbolt the rotor and protect it. A bent rotor is a real drag.
You are now ready to loosen the S&S couplings. Looking from the front of the bike, turn the coupling nut CCW with the spanner wrench.
Once the frame is disassembled, cover the tubes with the velcro frame pads and pack as follows.
All drawing are shown with the case on the ground and the top opened away from you.

(1) Place the middle frame section in the case as shown.

Tip: You can take an old tennis ball, cut an "X" in it and push it over any uncovered coupling for extra protection

Tip: Toe straps make great re-useable straps to keep frame sections and parts from moving around.

(2) Put the rear wheel in cassette side down. Be sure to add extra protection between the cassette cogs and the frame. Dense foam, plastic or several layers of cardboard will work.

(3) Intertwine the front and rear frame section as shown. Be sure to protect all metal-to-metal contact points.

(4) Place the front wheel in and as always, be sure to protect all metal-to-metal contact points.
All the rest of the parts will fit in the case. Figure out what works best for you and take lots of pictures.
Take care not to kink any cables or allow unprotected parts to  rub each other.
Take extra precautions: wrap the cranks in rags, stuff foam between parts, strap loose parts and frame sections together. Etc.

Re-assembly notes:
It is imperative that you understand were each part belongs and how the cables are routed. If you do not, take notes while you take the bike apart. Take pictures if you need to.  Install the timing chains while you re-install the left side cranks. It should not be necessary to readjust your derailleurs, brakes or eccentrics. If you have a bike equipped with a Travel Agent cable accelerator, you may need to rotate the pulley to get proper braking. Look at the position of the pulley before you disconnect the brakes.