Brian,
That gold-colored insert is your eccentric.
As far as your bottom bracket bearings are concerned, your eccentric is just like the threaded bottom bracket hanger in a conventional frame.
You'd leave the eccentric firmly clamped in your frame while you remove and install your bottom bracket cups.
The Shimano bottom bracket (as shown in the SJS Cycles link I gave above) has a plastic sleeve that fits between the separate left and right cups, inside the eccentric. It provides a measure of weather sealing from any water coming down the seatpost or in any open bottle bosses. To install this bottom bracket, you'd insert one half of the plastic sleeve in one cup and install the cup in your eccentric. Then, you'd do the same with the other. The plastic sleeves are...sleeved so one half slides over the other.
So to answer your question directly, the cups are separate and go in each side of your eccentric insert. The protective weather sleeve goes between the cups at time of installation.
Best,
Dan.